Visualizing Large-scale Copy Number Variation in Single-Cell RNA-Seq Expression Data

Timothy Tickle1, Itay Tirosh1,2, Christophe Georgescu1, Maxwell Brown1 and Brian Haas1

1Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
2Weizmann Institute of Science, Rehovot, Israel

2022-11-01

Abstract

InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for large-scale chromosomal copy number variations, such as gains or deletions of entire chromosomes or large segments of chromosomes. This is done by exploring expression intensity of genes across positions of the genome in comparison to the average or a set of reference ‘normal’ cells. A heatmap is generated illustrating the relative expression intensities across each chromosome, and it becomes readily apparent as to which regions of the genome are over-abundant or less-abundant as compared to normal cells (or the average, if reference normal cells are not provided).

Package

infercnv 1.15.0

1 Installation
2 Running InferCNV
- 2.1 Create the InferCNV Object
- 2.2 Running the full default analysis
3 Additional Information
4 Session info

1 Installation

1.1 Required dependencies

inferCNV uses the R packages ape, BiocGenerics, binhf, caTools, coda, coin, dplyr, doparallel, edgeR, fastcluster, fitdistrplus, foreach, futile.logger, future, gplots, ggplot2, HiddenMarkov, leiden, phyclust, RANN, reshape, rjags, RColorBrewer, SingleCellExperiment, SummarizedExperiment, tidyr and imports functions from the archived GMD.

1.2 Installing

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("infercnv")

1.3 Optional extension

If you want to use the interactive heatmap visualization, please check the add-on packge R inferCNV_NGCHM after installing the packages tibble, tsvio and NGCHMR. To install optional packages, type the following in an R command window:

install.packages("tibble")

install.packages("devtools")
devtools::install_github("bmbroom/tsvio")
devtools::install_github("bmbroom/NGCHMR", ref="stable")
devtools::install_github("broadinstitute/inferCNV_NGCHM")

And download the NGCHM java application by typing the following in a regular shell:

wget http://tcga.ngchm.net/NGCHM/ShaidyMapGen.jar

2 Running InferCNV

2.1 Create the InferCNV Object

Reading in the raw counts matrix and meta data, populating the infercnv object

infercnv_obj = CreateInfercnvObject(
  raw_counts_matrix="../inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz",
  annotations_file="../inst/extdata/oligodendroglioma_annotations_downsampled.txt",
  delim="\t",
  gene_order_file="../inst/extdata/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt",
  ref_group_names=c("Microglia/Macrophage","Oligodendrocytes (non-malignant)"))

## INFO [2022-11-01 18:12:14] Parsing matrix: ../inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz
## INFO [2022-11-01 18:12:16] Parsing gene order file: ../inst/extdata/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt
## INFO [2022-11-01 18:12:16] Parsing cell annotations file: ../inst/extdata/oligodendroglioma_annotations_downsampled.txt
## INFO [2022-11-01 18:12:16] ::order_reduce:Start.
## INFO [2022-11-01 18:12:16] .order_reduce(): expr and order match.
## INFO [2022-11-01 18:12:16] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 10338,184 Total=18322440.6799817 Min=0 Max=34215.
## INFO [2022-11-01 18:12:16] num genes removed taking into account provided gene ordering list: 399 = 3.8595473012188% removed.
## INFO [2022-11-01 18:12:16] -filtering out cells < 100 or > Inf, removing 0 % of cells
## WARN [2022-11-01 18:12:17] Please use "options(scipen = 100)" before running infercnv if you are using the analysis_mode="subclusters" option or you may encounter an error while the hclust is being generated.
## INFO [2022-11-01 18:12:17] validating infercnv_obj

2.2 Running the full default analysis

out_dir = tempfile()
infercnv_obj_default = infercnv::run(
    infercnv_obj,
    cutoff=1, # cutoff=1 works well for Smart-seq2, and cutoff=0.1 works well for 10x Genomics
    out_dir=out_dir,
    cluster_by_groups=TRUE, 
    plot_steps=FALSE,
    denoise=TRUE,
    HMM=FALSE,
    no_prelim_plot=TRUE,
    png_res=60
)

## Centering and scaling data matrix

## PC_ 1 
## Positive:  PSMD14, GCA, TANK, SCN2A, MARCH7, CSRNP3, TTC21B, SCN1A, SPC25, DHRS9 
##     BBS5, FASTKD1, PPIG, AKIRIN1, NDUFS5, RRAGC, MACF1, UTP11L, PPIEL, PHOSPHO2 
##     FHL3, PABPC4, SF3A3, PPIE, INPP5B, KLHL23, TRIT1, C1orf122, CAP1, MANEAL 
## Negative:  PPM1A, DHRS7, MNAT1, TRMT5, SLC38A6, HIF1A, SNAPC1, LINC00643, PCNXL4, DDHD1 
##     FERMT2, WDR89, GNPNAT1, GMFB, PPP2R5E, CGRRF1, STYX, RTN1, SOCS4, PSMC6 
##     MAPK1IP1L, FBXO34, ATG14, TXNDC16, JKAMP, KTN1, L3HYPDH, PELI2, C14orf166, KIAA0586 
## PC_ 2 
## Positive:  TMEM219, KCTD13, ASPHD1, TAOK2, SEZ6L2, HIRIP3, CDIPT, ALDOA, MVP, PAGR1 
##     PPP4C, PRRT2, MAZ, YPEL3, KIF22, QPRT, MAPK3, SULT1A4, SLX1B, CORO1A 
##     BOLA2, BOLA2B, SPNS1, SLX1A, NFATC2IP, SULT1A3, TUFM, CD2BP2, ATXN2L, TBC1D10B 
## Negative:  SEL1L, DIO2, NRXN3, ADCK1, GALC, SNW1, SPATA7, SLIRP, ZC3H14, ALKBH1 
##     TTC8, SPTLC2, FOXN3, AHSA1, EFCAB11, VIPAS39, TMED8, PSMC1, GSTZ1, POMT2 
##     CALM1, ZDHHC22, KIAA1737, RPS6KA5, ANGEL1, VASH1, C14orf159, GPATCH2L, TGFB3, SMEK1 
## PC_ 3 
## Positive:  CAND1, TMBIM4, DYRK2, MDM1, NUP107, RAP1B, LLPH, SLC35E3, LEMD3, MDM2 
##     CPM, GNS, CPSF6, LYZ, TBK1, YEATS4, XPOT, FRS2, C12orf66, SRGAP1 
##     CCT2, TMEM5, PPM1H, MON2, RAB3IP, USP15, CTDSP2, CNOT2, TSFM, METTL1 
## Negative:  RPL23A, SUPT6H, TRAF4, SDF2, FAM222B, KIAA0100, ALDOC, PIGS, ARHGEF26, ARHGEF26-AS1 
##     RAP2B, P2RY1, RNPC3, DPH5, MBNL1, SLC30A7, SLC44A1, ABCA1, FSD1L, EXTL2 
##     NIPSNAP3A, FKTN, RTCA, TMEM38B, HIAT1, P2RY12, SMC2, SLC35A3, ZNF462, KLF4 
## PC_ 4 
## Positive:  MRPL46, NTRK3, KLHL25, AKAP13, MRPS11, DET1, AEN, MFGE8, ABHD2, POLG 
##     PEX11A, AP3S2, IDH2, C15orf38-AP3S2, C15orf38, CIB1, NGRN, CRTC3, MAN2A2, UNC45A 
##     HDDC3, VPS33B, CHD2, RGMA, IGF1R, LRRC28, MEF2A, LINS, ASB7, VIMP 
## Negative:  RBM12, NFS1, CPNE1, ROMO1, ERGIC3, CEP250, EIF6, RBM39, EDEM2, TRPC4AP 
##     PHF20, GSS, SCAND1, ACSS2, LINC00657, GGT7, EPB41L1, TP53INP2, AAR2, NCOA6 
##     DLGAP4, PIGU, C20orf24, NDRG3, MAP1LC3A, SOGA1, DYNLRB1, SAMHD1, ITCH, RBL1 
## PC_ 5 
## Positive:  STX17, ERP44, NR4A3, INVS, SEC61B, TEX10, ALG2, MSANTD3, MSANTD3-TMEFF1, TGFBR1 
##     LPPR1, TBC1D2, MRPL50, TRIM14, ZNF189, NANS, ANP32B, TMEM246, C9orf156, RNF20 
##     XPA, SMC2, NCBP1, NIPSNAP3A, TSTD2, ABCA1, TMOD1, SLC44A1, ZNF510, FSD1L 
## Negative:  ZNF160, ZNF415, ZNF83, ZNF331, MYADM, ZNF528, NDUFA3, ZNF880, ZNF610, ZNF480 
##     TFPT, PRPF31, LENG1, MBOAT7, TSEN34, RPS9, LILRA4, LAIR1, TTYH1, LENG8 
##     LILRB4, RDH13, HSPBP1, RPL28, SHISA7, ISOC2, ZNF580, ZNF581, ZNF542, ZNF583

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  RFC1, RPL9, KLHL5, LIAS, UGDH, TMEM156, UGDH-AS1, TLR1, KLF3, SMIM14 
##     PGM2, RELL1, UBE2K, ARAP2, TBC1D19, PDS5A, RBPJ, APBB2, ANAPC4, DHX15 
##     UCHL1, PACRGL, LCORL, DCAF16, LIMCH1, MED28, LAP3, TMEM33, QDPR, TAPT1-AS1 
## Negative:  PNPLA2, RPLP2, CD151, PIDD, SLC25A22, CEND1, POLR2L, PDDC1, TALDO1, CHID1 
##     TMEM80, TOLLIP, DEAF1, IRF7, MOB2, PHRF1, SNHG9, RPS2, IFITM10, TBL3 
##     NDUFB10, NTHL1, MSRB1, FAHD1, NUBP2, HAGH, SPSB3, MRPS34, TSC2, CRAMP1L 
## PC_ 2 
## Positive:  APC2, C19orf25, MBD3, UQCR11, SCAMP4, BTBD2, MOB3A, AP3D1, PLEKHJ1, RNPS1 
##     ECI1, E4F1, ABCA3, TBC1D24, ATP6V0C, MLST8, TRAF7, AMDHD2, SF3A2, PKD1 
##     TSC2, NTHL1, TBL3, SNHG9, CEMP1, RPS2, NDUFB10, OAZ1, MSRB1, FAHD1 
## Negative:  ZNF131, NIM1, NIPBL, SLC1A3, SEPP1, HMGCS1, SKP2, C5orf42, FBXO4, LMBRD2 
##     C5orf28, C5orf51, NUP155, BRIX1, PAIP1, WDR70, RAD1, OXCT1, NNT, LIFR 
##     AMACR, RPL37, RICTOR, TARS, FYB, MRPS30, DAB2, PRKAA1, SUB1, TTC33 
## PC_ 3 
## Positive:  PSMC5, TEX2, CCDC47, POLG2, FTSJ3, STRADA, DDX42, DDX5, TACO1, MIR3064 
##     MIR5047, DCAF7, CEP95, TANC2, SMURF2, PLEKHM1P, METTL2A, LRRC37A3, MED13, AMZ2P1 
##     INTS2, BCAS3, GNA13, PRKCA, PPM1D, CACNG4, APPBP2, HELZ, PSMD12, USP32 
## Negative:  PODXL2, MCM2, TPRA1, MGLL, PLXNA1, SEC61A1, CHCHD6, ZXDC, RUVBL1, SLC41A3 
##     CCDC14, KALRN, OSBPL11, UMPS, SNX4, ZNF148, EEFSEC, MYLK, PTPLB, RPN1 
##     SEC22A, RAB7A, SEMA5B, ACAD9, HSPBAP1, ISY1, DTX3L, CNBP, PARP9, COPG1 
## PC_ 4 
## Positive:  MOSPD3, ACTL6B, GNB2, GIGYF1, TSC22D4, POP7, C7orf61, MEPCE, ZCWPW1, SLC12A9 
##     PILRA, PILRB, TRIP6, SRRT, ACHE, AP1S1, PLOD3, ZNHIT1, FIS1, RABL5 
##     CUX1, PRKRIP1, ORAI2, ALKBH4, NDN, MKRN3, SNRPN, SNURF, HERC2P7, UBE3A 
## Negative:  SYNJ2BP, MED6, COX16, SMOC1, SRSF5, PCNX, KIAA0247, ZFYVE1, RBM25, PSEN1 
##     NUMB, ACOT2, PNMA1, ELMSAN1, PTGR2, CRY1, MTERFD3, ZNF410, C12orf23, RIC8B 
##     POLR3B, FAM161B, TCP11L2, CKAP4, COQ6, C12orf75, ALDH6A1, APPL2, LIN52, ABCD4 
## PC_ 5 
## Positive:  FGFR1OP, RNASET2, RPS6KA2, MLLT4, MPC1, SFT2D1, THBS2, QKI, C6orf120, CAHM 
##     LINC00574, AGPAT4, DLL1, FAM120B, MAP3K4, PSMB1, TBP, LPAL2, PDCD2, MRPL18 
##     TCP1, SRD5A1, MTRR, NSUN2, CCDC127, MED10, SDHA, FASTKD3, MRPL36, PDCD6 
## Negative:  SEC61B, NR4A3, ALG2, STX17, TGFBR1, TBC1D2, ERP44, TRIM14, NANS, INVS 
##     ANP32B, ECHDC1, RNF146, TEX10, KIAA0408, TRMT11, HINT3, NCOA7, C9orf156, MSANTD3 
##     PTPRK, MSANTD3-TMEFF1, EPB41L2, XPA, LPPR1, AKAP7, MRPL50, ZNF189, TMEM246, NCBP1

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  NTHL1, TBL3, SNHG9, RPS2, NDUFB10, MSRB1, FAHD1, HAGH, NUBP2, SPSB3 
##     MRPS34, NME3, MAPK8IP3, CRAMP1L, TELO2, CLCN7, C16orf91, UNKL, GNPTG, BAIAP3 
##     UBE2I, SOX8, LMF1, CHTF18, RPUSD1, NARFL, HAGHL, WSCD1, MIS12, C1QBP 
## Negative:  NFASC, MDM4, CNTN2, PIK3C2B, RBBP5, PPP1R15B, DSTYK, TMCC2, SNRPE, ZBED6 
##     CDK18, ZC3H11A, NUCKS1, ATP2B4, RAB7L1, BTG2, SLC41A1, ADORA1, SRGAP2, TMEM183A 
##     GLMN, BTBD8, RPAP2, CDC7, ZNF644, RPL5, ZNF326, CYB5R1, LRRC8D, EIF2D 
## PC_ 2 
## Positive:  GBA2, CREB3, TLN1, CCDC107, RUSC2, STOML2, PIGO, FANCG, VCP, DNAJB5 
##     IL11RA, KIAA1161, FAM219A, GALT, NUDT2, RPP25L, DCTN3, SIGMAR1, UBAP1, ATP5H 
##     ARMC7, DCAF12, ICT1, NT5C, HN1, UBAP2, CDR2L, SUMO2, HID1, UBE2R2 
## Negative:  CD27-AS1, TNFRSF1A, TAPBPL, VAMP1, NACA, MRPL51, PRIM1, SNORA48, PARP11, LRP1 
##     TULP3, RHNO1, SHMT2, NRIP2, R3HDM2, ITFG2, FKBP4, ARHGAP9, DCP1B, MARS 
##     ADIPOR2, DDIT3, ERC1, RAD52, DCTN2, WNK1, KIF5A, PIP4K2C, NINJ2, DTX3 
## PC_ 3 
## Positive:  IFI27L2, KIAA0196, SQLE, NSMCE2, DICER1, MTSS1, DDX24, TRIB1, NDUFB9, DICER1-AS1 
##     FAM84B, TATDN1, SNHG10, RNF139, UNC79, GLRX5, TRMT12, MYC, FAM91A1, UBR7 
##     C14orf132, FAM49B, WDYHV1, ATG2B, ZHX1, ASAP1, C14orf142, C8orf76, GSKIP, EFR3A 
## Negative:  TSTD2, NCBP1, XPA, C9orf156, ANP32B, NANS, TRIM14, TBC1D2, TGFBR1, ALG2 
##     SEC61B, NR4A3, STX17, ERP44, INVS, TEX10, MSANTD3, MSANTD3-TMEFF1, LPPR1, MRPL50 
##     COMMD1, CCT4, B3GNT2, FAM161A, EHBP1, WDPCP, TIA1, C2orf42, XPO1, ZNF189 
## PC_ 4 
## Positive:  ACSS2, GSS, GGT7, TRPC4AP, TP53INP2, NCOA6, EDEM2, PIGU, EIF6, CEP250 
##     MAP1LC3A, ERGIC3, CPNE1, DYNLRB1, RBM12, NFS1, ITCH, ROMO1, RBM39, PHF20 
##     AHCY, VPS29, SCAND1, FAM216A, LINC00657, EIF2S2, GPN3, EPB41L1, AAR2, ARPC3 
## Negative:  POLG, ABHD2, PEX11A, MFGE8, AEN, AP3S2, DET1, C15orf38-AP3S2, MRPS11, C15orf38 
##     MAN2A2, UNC45A, CRTC3, IDH2, NGRN, MRPL46, HDDC3, CIB1, VPS33B, NTRK3 
##     CHD2, RGMA, KLHL25, AKAP13, IGF1R, ZNF592, SEC11A, NMB, LRRC28, WDR73 
## PC_ 5 
## Positive:  SGTB, NLN, TRAPPC13, TRIM23, PPWD1, CWC27, RNF180, IPO11, DIMT1, KIF2A 
##     ZSWIM6, SMIM15, ADAMTS1, NDUFAF2, APP, N6AMT1, LTN1, GABPA, ATP5J, RWDD2B 
##     ERCC8, JAM2, USP16, PLK2, CCT8, MRPL39, BACH1, TIAM1, NCAM2, GPBP1 
## Negative:  MFNG, CDC42EP1, GGA1, PDXP, LGALS1, H1F0, GCAT, ANKRD54, EIF3L, POLR2F 
##     PLA2G6, MAFF, TMEM184B, CSNK1E, DDX17, CBY1, TOMM22, JOSD1, GTPBP1, SUN2 
##     DNAL4, NPTXR, PDGFB, RPL3, SYNGR1, TAB1, ATF4, RPS19BP1, TNRC6B, ADSL

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  BANP, KLHDC4, MAP1LC3B, IRF8, COX4I1, EMC8, CRISPLD2, USP10, COTL1, SUDS3 
##     TAOK3, PEBP1, VSIG10, WSB2, TAF1C, RFC5, FBXO21, JRK, FBXW8, CASP2 
##     GSTK1, FAM131B, MTRNR2L6, RNFT2, ZFYVE27, ARC, CRTAC1, AVPI1, ZYX, R3HCC1L 
## Negative:  SCFD2, FIP1L1, DANCR, SGCB, DCUN1D4, OCIAD1, CHIC2, FRYL, PDGFRA, NFXL1 
##     SRD5A3, COMMD8, GNPDA2, TMEM165, GUF1, CLOCK, ATP8A1, EXOC1, AASDH, PPAT 
##     SLC30A9, PAICS, SRP72, NOA1, POLR2B, LPHN3, UBA6, YTHDC1, TMEM33, UTP3 
## PC_ 2 
## Positive:  PLD2, PSMB6, SLC25A11, CXCL16, RNF167, ARRB2, PELP1, MED11, PFN1, MYBBP1A 
##     XAF1, SPAG7, UBE2G1, C17orf100, TXNDC17, RNASEK, WSCD1, ANKFY1, CAMTA2, MIS12 
##     C17orf49, ZFP3, DERL2, RPAIN, ZNF232, CYB5D2, ACADVL, C1QBP, ZNF594, NUP88 
## Negative:  COG1, FAM104A, CD300A, SSTR2, C17orf80, BTBD17, SLC39A11, SOX9, CDC42EP4, SLC9A3R1 
##     KCNJ16, TTYH2, RPL38, ABCA8, PRKAR1A, NAT9, AMZ2, LINC00674, KPNA2, TMEM104 
##     C17orf58, BPTF, FDXR, NOL11, PSMD12, HID1, HELZ, CDR2L, CACNG4, PRKCA 
## PC_ 3 
## Positive:  APLP2, NFRKB, ZBTB44, SNX19, NTM, IGSF9B, JAM3, NCAPD3, VPS26B, THYN1 
##     ACAD8, B3GAT1, SYNJ2BP, MED6, PCNX, ZFYVE1, RBM25, PSEN1, NUMB, ACOT2 
##     PNMA1, EML1, CYP46A1, ELMSAN1, EVL, YY1, CCNK, PTGR2, FAM161B, COQ6 
## Negative:  FAM21C, AGAP4, PARG, ZNF485, ALOX5, VSTM4, CXCL12, ZNF32, ZNF22, ZNF239 
##     NCOA4, RASSF4, ARHGAP22, BMS1P1, HNRNPF, GLUD1P7, MAPK8, FAM21B, BMS1P2, BMS1P6 
##     AGAP9, ZNF488, BMS1P5, CSGALNACT2, TIMM23, BMS1, ZNF33B, AGAP6, ZNF37BP, HSD17B7P2 
## PC_ 4 
## Positive:  GEMIN2, TRAPPC6B, PNN, CTAGE5, SEC23A, KLHL28, LINC00639, FAM179B, TMX1, TRIM9 
##     NIN, PYGL, PRPF39, MBIP, ATL1, MAP4K5, FKBP3, ATP5S, MDGA2, RPS29 
##     MIS18BP1, BRMS1L, RPL36AL, L2HGDH, MGAT2, DNAAF2, ARF6, NEMF, KLHDC1, KLHDC2 
## Negative:  TBXAS1, SLC37A3, LUC7L2, HIPK2, C7orf55, MKRN1, UBN2, NDUFB2, ZC3HAV1, BRAF 
##     TRIM24, AHSA2, USP34, CREB3L2, C2orf74, XPO1, MRPS33, PEX13, FAM161A, DGKI 
##     REL, CCT4, AGK, TMED8, PTN, VIPAS39, AHSA1, COMMD1, GSTZ1, SPTLC2 
## PC_ 5 
## Positive:  SYNJ2BP, MED6, PCNX, ZFYVE1, RBM25, PSEN1, NUMB, ACOT2, PNMA1, ELMSAN1 
##     PTGR2, ZNF410, FAM161B, COQ6, ALDH6A1, LIN52, UBIAD1, MTOR, EXOSC10, SRM 
##     TARDBP, DFFA, PGD, KIF1B, ABCD4, UBE4B, NMNAT1, CNTLN, PSIP1, SNAPC3 
## Negative:  NUP88, RPAIN, RABEP1, ZNF594, C1QBP, ZNF232, DERL2, ZFP3, CAMTA2, MIS12 
##     SPAG7, WSCD1, PFN1, TXNDC17, RNF167, SLC25A11, PLD2, C17orf100, PSMB6, CXCL16 
##     XAF1, MED11, ARRB2, RNASEK, PELP1, MYBBP1A, UBE2G1, C17orf49, MARCH5, EXOC6

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  CHRNB1, NLGN2, ZBTB4, TMEM256, POLR2A, GPS2, EIF4A1, EIF5A, CTDNEP1, GABARAP 
##     PHF23, DVL2, ACADVL, C17orf49, RNASEK, XAF1, ZNF594, RABEP1, C17orf100, ZNF232 
##     NUP88, TXNDC17, RPAIN, DERL2, ZFP3, MIS12, C1QBP, WSCD1, CAMTA2, AMZ1 
## Negative:  MRPL42, UBE2N, CRADD, EEA1, CCDC41, ACTR6, SCYL2, BTG1, TMCC3, ANO4 
##     ATP2B1, NDUFA12, ARL1, NR2C1, GNPTAB, POC1B, CCDC53, NUP37, DUSP6, ASCL1 
##     NT5DC3, C12orf29, HSP90B1, RSU1, STAM, C12orf73, FAM188A, NSUN6, CCDC59, ARL5B 
## PC_ 2 
## Positive:  PTPN1, ADNP, TMEM189, DPM1, UBE2V1, MOCS3, ATP9A, RNF114, ZFP64, BCAS1 
##     SLC9A8, ZFAS1, ARFGEF2, PFDN4, CSE1L, ZNFX1, STAU1, DDX27, DOK5, CSTF1 
##     RTFDC1, BMP7, RAE1, MTRNR2L3, VAPB, STX16, NPEPL1, ATP5J2, ZNF789, ZNF394 
## Negative:  ING2, RWDD4, CDKN2AIP, AGA, TRAPPC11, SPCS3, STOX2, GPM6A, SH3D19, PET112 
##     RPS3A, ARFIP1, TRIM2, FBXW7, KIAA0922, DCLK2, GLRA3, TLR2, PRMT10, ZKSCAN8 
##     PLRG1, IRF2, TMEM184C, CTSO, SLC10A7, CEP44, LSM6, PDGFC, ZSCAN9, FBXO8 
## PC_ 3 
## Positive:  ATP6V1H, RB1CC1, TCEA1, PCMTD1, LYPLA1, UBE2V2, MRPL15, TMEM68, TGS1, ERLIN2 
##     PROSC, DUSP26, BRF2, RNF122, RPS20, EIF4EBP1, MAK16, ASH2L, TTI2, FUT10 
##     LSM1, CHCHD7, PPP2CB, BAG4, IMPAD1, DDHD2, ZCCHC8, UBXN8, CLIP1, VPS33A 
## Negative:  TBK1, GNS, XPOT, LEMD3, C12orf66, LLPH, TMBIM4, CAND1, DYRK2, SRGAP1 
##     MDM1, RAP1B, TMEM5, NUP107, NMI, RND3, RIF1, SLC35E3, PPM1H, MMADHC 
##     KIF5C, ARL5A, EPC2, CACNB4, STAM2, MDM2, MON2, PAPOLA, VRK1, GSKIP 
## PC_ 4 
## Positive:  TRPC4AP, GSS, EDEM2, EIF6, ACSS2, CEP250, CPNE1, ERGIC3, GGT7, RBM12 
##     NFS1, TP53INP2, ROMO1, NCOA6, RBM39, PIGU, PHF20, MAP1LC3A, DYNLRB1, SCAND1 
##     ITCH, LINC00657, AHCY, EPB41L1, AAR2, EIF2S2, DLGAP4, RALY, C20orf24, PXMP4 
## Negative:  GCC2, ST6GAL2, LIMS1, UXS1, RANBP2, NCK2, SEPT10, C2orf49, RGPD5, GPR45 
##     LINC00116, MRPS9, MERTK, MAP4K4, RNF149, ZC3H8, RPL31, PDCL3, TTL, CHST10 
##     AFF3, REV1, EIF5B, TXNDC9, MRPL30, MITD1, MGAT4A, LIPT1, NR1H3, ACP2 
## PC_ 5 
## Positive:  GOT1, SLC25A28, CUTC, COX15, DNMBP, HPS1, ERLIN1, CHUK, CWF19L1, BLOC1S2 
##     SFXN2, WBP1L, SCD, ARL3, R3HCC1L, C10orf32, TRIM8, LINC00263, AS3MT, NT5C2 
##     DCTPP1, LDB1, SEC31B, ACTR1A, PPRC1, NOLC1, GBF1, INA, FBXL15, TMEM180 
## Negative:  MED28, DCAF16, LCORL, PACRGL, LAP3, DHX15, ANAPC4, QDPR, RBPJ, TBC1D19 
##     TAPT1-AS1, ARAP2, RELL1, FAM200B, PGM2, FBXL5, KLF3, TLR1, CC2D2A, TMEM156 
##     RAB28, KLHL5, WDR1, RFC1, RPL9, ACOX3, LIAS, SH3TC1, UGDH, UGDH-AS1

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  MTX1, KRTCAP2, GBAP1, DPM3, GBA, SCAMP3, SLC50A1, CLK2, FDPS, EFNA1 
##     RUSC1, ASH1L, ADAM15, YY1AP1, DAP3, MSTO1, GON4L, FLAD1, SYT11, CKS1B 
##     RIT1, KIAA0907, SHC1, ARHGEF2, SSR2, PYGO2, UBQLN4, PMVK, LAMTOR2, ADAR 
## Negative:  CELSR2, PSRC1, SARS, SORT1, TMEM167B, WDR47, CLCC1, GPSM2, STXBP3, PRPF38B 
##     PRMT6, AMY2B, RNPC3, DPH5, SLC30A7, EXTL2, RTCA, GSTM3, HIAT1, CAP1 
##     PPT1, TRIT1, RLF, COL9A2, ZMPSTE24, PPIE, PABPC4, SMAP2, SLC35A3, CSF1 
## PC_ 2 
## Positive:  RAB4A, RHOU, NUP133, RNF187, TAF5L, GALNT2, COG2, TRIM11, AGT, C1orf198 
##     GUK1, TTC13, MRPL55, ARV1, C1orf35, C1orf131, ARF1, SCAMP3, GBA, CLK2 
##     FDPS, RUSC1, GBAP1, GNPAT, ASH1L, MTX1, JMJD4, EXOC8, MSTO1, SPRTN 
## Negative:  SOAT1, TOR1AIP2, SNORA67, ABL2, TOR1AIP1, TOR3A, CEP350, QSOX1, RASAL2, ACBD6 
##     ASTN1, XPR1, RFWD2, TNR, STX6, MRPS14, CACNA1E, CACYBP, RABGAP1L, GLUL 
##     RC3H1, ZBTB37, NPL, GAS5, DHX9, NMNAT2, DARS2, SMG7, KLHL20, ARPC5 
## PC_ 3 
## Positive:  SHC1, CKS1B, FLAD1, PYGO2, ADAM15, EFNA1, PMVK, SLC50A1, ADAR, DPM3 
##     C1orf43, CHRNB2, HAX1, UBAP2L, KRTCAP2, GBA, SCAMP3, CLK2, MTX1, GBAP1 
##     FDPS, RUSC1, ASH1L, MSTO1, YY1AP1, DAP3, GON4L, SYT11, RIT1, KIAA0907 
## Negative:  IL10, EIF2D, SRGAP2, SLC41A1, CD55, RAB7L1, NUCKS1, CD46, CDK18, HSD11B1 
##     TMCC2, DSTYK, SYT14, RBBP5, RCOR3, CNTN2, INTS7, NFASC, RPL21P28, TMEM206 
##     MDM4, PIK3C2B, NENF, SNRPE, ZBED6, PPP1R15B, ATF3, ZC3H11A, NSL1, ANGEL2 
## PC_ 4 
## Positive:  PMF1-BGLAP, PMF1, SLC25A44, LMNA, PAQR6, LAMTOR2, SMG5, UBQLN4, SSR2, C1orf85 
##     CCT3, C1orf61, ARHGEF2, MEF2D, APOA1BP, KIAA0907, GPATCH4, RIT1, BCAN, SYT11 
##     ISG20L2, GON4L, RRNAD1, DAP3, MRPL24, YY1AP1, HDGF, MSTO1, PRCC, ASH1L 
## Negative:  IFI44, TTLL7, DNAJB4, PRKACB, RPF1, CLCA4, GTF2B, SH3GLB1, ODF2L, PKN2 
##     GNG5, DDAH1, SEP15, FUBP1, CCBL2, BCL10, C1orf52, LRRC8D, ZNF326, FAM73A 
##     USP33, ZNF644, CDC7, ZZZ3, AK5, BTBD8, PIGK, GLMN, RPAP2, ST6GALNAC3 
## PC_ 5 
## Positive:  RBM8A, LIX1L, GNRHR2, POLR3GL, PEX11B, TXNIP, PIAS3, NOTCH2NL, POLR3C, RNF115 
##     NUDT4P1, GPR89A, SEC22B, PRKAB2, PDE4DIP, CHD1L, PFN1P2, BCL9, GPR89B, LINC00623 
##     NBPF24, SRGAP2C, NBPF15, FCGR1B, NBPF16, FCGR1C, NOTCH2, FCGR1A, PHGDH, HIST2H2BF 
## Negative:  RIT1, SYT11, GON4L, KIAA0907, DAP3, YY1AP1, ARHGEF2, MSTO1, ASH1L, SSR2 
##     RUSC1, FDPS, UBQLN4, CLK2, LAMTOR2, LRRC47, RPL22, DFFB, WRAP73, ICMT 
##     C1orf174, ACOT7, PANK4, LMNA, SCAMP3, PEX10, NOL9, KLHL21, THAP3, RER1

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  PLEKHH2, DYNC2LI1, ZFP36L2, LRPPRC, THADA, PPM1B, MTA3, PREPL, COX7A2L, SRBD1 
##     PIGF, EML4, CRIPT, SOCS5, MCFD2, SLC8A1, CALM2, BCYRN1, MSH2, MSH6 
##     THUMPD2, FBXO11, RTN4, FOXN2, SPTBN1, RPS27A, ACYP2, PPP1R21, TMEM178A, NRXN1 
## Negative:  USP40, DGKD, ATG16L1, INPP5D, GIGYF2, EFHD1, EIF4E2, TIGD1, DIS3L2, COPS7B 
##     PDE6D, PTMA, NCL, ARMC9, PSMD1, ITM2C, CAB39, SP100, SP110, FBXO36 
##     TRIP12, DNER, PID1, SPHKAP, MFF, RHBDD1, DOCK10, CUL3, SERPINE2, MRPL44 
## PC_ 2 
## Positive:  BCS1L, ZNF142, RNF25, RQCD1, STK36, USP37, CTDSP1, TTLL4, SLC11A1, CYP27A1 
##     TMBIM1, NHEJ1, PNKD, AAMP, ARPC2, CNPPD1, TNS1, RPL37A, FAM134A, SMARCAL1 
##     ZFAND2B, XRCC5, TMEM169, ABCB6, PECR, ATG9A, ANKZF1, ATIC, DNAJB2, SPAG16 
## Negative:  SFXN5, SMYD5, SPR, EXOC6B, ZNF638, PRADC1, MPHOSPH10, CCT7, MCEE, NAGK 
##     ALMS1, TEX261, TPRKB, VAX2, DUSP11, ADD2, STAMBP, TGFA, DGUOK, FAM136A 
##     BOLA3, PNO1, PPP3R1, PLEK, NFU1, GFPT1, WDR92, ANTXR1, ANXA4, CNRIP1 
## PC_ 3 
## Positive:  CCDC115, IMP4, MZT2B, PTPN18, FAM168B, ARHGEF4, SMPD4, PLEKHB2, MZT2A, C2orf27A 
##     HS6ST1, CCNT2, NCKAP5, RAB3GAP1, R3HDM1, UBXN4, UGGT1, SAP130, AMMECR1L, POLR2D 
##     EPC2, KIF5C, MMADHC, WDR33, RND3, NMI, RIF1, GPR17, ARL5A, CACNB4 
## Negative:  DOK1, POLE4, LOXL3, MRPL19, HTRA2, AUP1, GCFC2, PCGF1, LRRTM4, CTNNA2 
##     TTC31, CCDC142, SUCLG1, MRPL53, MOGS, TMSB10, WBP1, TGOLN2, RTKN, RETSAT 
##     WDR54, DCTN1, ELMOD3, MTHFD2, CAPG, MOB1A, MAT2A, BOLA3-AS1, GGCX, BOLA3 
## PC_ 4 
## Positive:  RAB1A, ACTR2, SPRED2, CEP68, MEIS1, AFTPH, PELI1, UGP2, ETAA1, MDH1 
##     C1D, WDPCP, WDR92, EHBP1, PNO1, B3GNT2, PPP3R1, CNRIP1, COMMD1, PLEK 
##     CCT4, ANTXR1, FAM161A, GFPT1, XPO1, NFU1, USP34, ANXA4, AHSA2, GMCL1 
## Negative:  RNF149, RPL31, MAP4K4, PDCL3, MRPS9, CHST10, GPR45, AFF3, C2orf49, NCK2 
##     REV1, UXS1, EIF5B, ST6GAL2, GCC2, TXNDC9, LIMS1, MRPL30, RANBP2, SEPT10 
##     MITD1, RGPD5, LINC00116, LIPT1, MERTK, MGAT4A, ZC3H8, TTL, POLR1B, CHCHD5 
## PC_ 5 
## Positive:  UCN, MPV17, CAD, GTF3C2, ATRAID, EIF2B4, SNX17, SLC5A6, PPM1G, PREB 
##     NRBP1, CGREF1, IFT172, KHK, ZNF512, OST4, CCDC121, AGBL5, GPN1, TMEM214 
##     MAPRE3, SUPT7L, DPYSL5, SLC4A1AP, SLC35F6, MRPL33, KCNK3, EPT1, BRE, HADHB 
## Negative:  BIN1, GYPC, ERCC3, CNTNAP5, MKI67IP, TSN, IWS1, CLASP1, LIMS2, POLR2D 
##     WDR33, AMMECR1L, GPR17, RALB, SAP130, EPB41L5, UGGT1, DBI, INSIG2, HS6ST1 
##     CCDC93, SMPD4, DDX18, CBWD2, IL1A, IL1B, SLC20A1, ACTR3, CHCHD5, POLR1B

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  TMEM115, C3orf18, CYB561D2, HEMK1, NPRL2, MAPKAPK3, SEMA3B, IFRD2, RASSF1, GNAI2 
##     MANF, TUSC2, HYAL2, NAT6, SLC38A3, VPRBP, RBM5, RAD54L2, RBM6, TEX264 
##     MON1A, RRP9, UBA7, PARP3, GPR62, PCBP4, FAM212A, ABHD14B, IP6K1, ABHD14A 
## Negative:  ATP6V1A, NAA50, KIAA2018, MIR568, SPICE1, ZBTB20, GAP43, C3orf17, LSAMP, GTPBP8 
##     SLC35A5, IGSF11, ATG3, B4GALT4, CD200, ARHGAP31, ABHD10, PVRL3, TMEM39A, DZIP3 
##     POGLUT1, IFT57, TIMMDC1, CD47, BBX, COX17, CBLB, GSK3B, ALCAM, LRRC58 
## PC_ 2 
## Positive:  CHMP2B, CADM2, CGGBP1, GBE1, ZNF654, C3orf38, ROBO1, PROS1, DHFRL1, FAM86DP 
##     NSUN3, PPP4R2, CLDND1, SHQ1, ST3GAL6, FOXP1, ARL6IP5, CMSS1, TBC1D23, UBA3 
##     NIT2, TMF1, TOMM70A, LNP1, SUCLG2, TMEM45A, TFG, KBTBD8, SENP7, LRIG1 
## Negative:  CCDC174, LSM3, XPC, TMEM43, CHCHD4, METTL6, HDAC11, EAF1, HACL1, IQSEC1 
##     BTD, ANKRD28, GALNT15, RPL32, DPH3, GORASP1, WDR48, CSRNP1, OXSM, CX3CR1 
##     EXOG, OXNAD1, NKIRAS1, NGLY1, SLC4A7, SLC25A38, RPL15, UBE2E1, TOP2B, NR1D2 
## PC_ 3 
## Positive:  RFT1, TKT, NEK4, DCP1A, CHDH, SPCS1, IL17RB, GLT8D1, ACTR8, GNL3 
##     PBRM1, SELK, NT5DC2, ERC2, STAB1, CCDC66, NISCH, BAP1, FAM208A, GLYCTK 
##     WDR82, IL17RD, TWF2, APPL1, ALAS1, DUSP7, PDE12, RPL29, ARF4, ACY1 
## Negative:  AZI2, STT3B, GPD1L, CMTM7, CMC1, CMTM6, SLC4A7, DYNC1LI1, CNOT10, OXSM 
##     GLB1, NGLY1, TMPPE, TOP2B, CRTAP, NR1D2, SUSD5, FBXL2, RPL15, CLASP2 
##     PDCD6IP, ARPP21, NKIRAS1, EPM2AIP1, MLH1, UBE2E1, LRRFIP2, GOLGA4, UBE2E2, PLCD1 
## PC_ 4 
## Positive:  VPS8, MAGEF1, C3orf70, MAP3K13, POLR2H, FAM131A, TMEM41A, EIF4G1, SENP2, TRA2B 
##     PSMD2, ETV5, ECE2, DGKG, ALG3, TBCCD1, ABCF3, DNAJB11, AP2M1, EIF4A2 
##     DVL3, RFC4, ST6GAL1, EIF2B5, MASP1, ABCC5, BCL6, PARL, LPP, IL1RAP 
## Negative:  ACAA1, MYD88, PLCD1, GOLGA4, OXSR1, EXOG, WDR48, GORASP1, LRRFIP2, CSRNP1 
##     MLH1, CX3CR1, SLC25A38, EPM2AIP1, RPSA, ARPP21, MOBP, EIF1B, PDCD6IP, CLASP2 
##     RPL14, FBXL2, SUSD5, CRTAP, TMPPE, ZNF619, GLB1, CNOT10, DYNC1LI1, ZNF620 
## PC_ 5 
## Positive:  ATG7, SLC6A1, VGLL4, SEC13, TAMM41, IRAK2, VHL, TIMP4, TSEN2, BRK1 
##     CIDECP, MKRN2, EMC3, CRELD1, RAF1, CAND2, JAGN1, RPL32, RPUSD3, IQSEC1 
##     HDAC11, TTLL3, CHCHD4, ARPC4, TMEM43, TADA3, XPC, LSM3, CAMK1, CCDC174 
## Negative:  MYLK, CCDC14, PTPLB, SEC22A, KALRN, SEMA5B, HSPBAP1, UMPS, DTX3L, ZNF148 
##     PARP9, SNX4, OSBPL11, KPNA1, SLC41A3, WDR5B, ZXDC, FAM162A, CHCHD6, CCDC58 
##     PLXNA1, CD86, TPRA1, SLC15A2, MCM2, IQCB1, PODXL2, GOLGB1, MGLL, HCLS1

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  FAM149A, UFSP2, ANKRD37, KIAA1430, SLC25A4, ACSL1, CASP3, IRF2, STOX2, TRAPPC11 
##     RWDD4, ING2, CDKN2AIP, AGA, SPCS3, GPM6A, GLRA3, CEP44, FBXO8, SCRG1 
##     TMEM184C, SLC10A7, PRMT10, C4orf48, LSM6, DCLK2, RPS3A, HMGB2, SH3D19, AADAT 
## Negative:  APBB2, SLC30A9, UCHL1, LIMCH1, TMEM33, PDS5A, ATP8A1, UBE2K, GUF1, GNPDA2 
##     SMIM14, COMMD8, UGDH-AS1, NFXL1, UGDH, FRYL, LIAS, OCIAD1, RPL9, DCUN1D4 
##     RFC1, SGCB, KLHL5, DANCR, TMEM156, TLR1, SCFD2, KLF3, FIP1L1, PGM2 
## PC_ 2 
## Positive:  CBR4, SPOCK3, CPE, SH3RF1, NEK1, CLCN3, C4orf27, MSMO1, MFAP3L, AADAT 
##     HMGB2, TMEM192, SCRG1, FAM218A, FBXO8, MARCH1, CEP44, TMA16, GLRA3, NAF1 
##     GPM6A, RAPGEF2, SPCS3, PPID, ETFDH, AGA, TMEM144, CDKN2AIP, GRIA2, ING2 
## Negative:  TMEM156, TLR1, KLHL5, KLF3, RFC1, LAP3, QDPR, TAPT1-AS1, PGM2, RPL9 
##     MED28, FAM200B, PACRGL, DHX15, DCAF16, ANAPC4, RELL1, LCORL, RBPJ, FBXL5 
##     LIAS, TBC1D19, ARAP2, CC2D2A, UGDH, RAB28, UGDH-AS1, WDR1, ACOX3, SMIM14 
## PC_ 3 
## Positive:  HELQ, COQ2, MRPS18C, COPS4, FAM175A, ARHGAP24, MAPK10, THAP9, KLHL8, THAP9-AS1 
##     HSD17B11, NUDT9, SEC31A, SPARCL1, SPP1, SCD5, PKD2, PPM1K, PYURF, ENOPH1 
##     HERC3, HNRNPD, PIGY, RASGEF1B, NAP1L5, MRPL1, FAM13A, CCNI, SNCA, FAM47E 
## Negative:  MFSD10, LRPAP1, RGS12, ADD1, TMEM128, TNIP2, LYAR, FAM193A, ZBTB49, NSG1 
##     RNF4, STX18, CYTL1, MXD4, CRMP1, HAUS3, WFS1, C4orf48, MAN2B2, MRFAP1 
##     MRFAP1L1, BLOC1S4, KIAA0232, TBC1D14, TADA2B, GRPEL1, AFAP1, SH3TC1, ACOX3, WDR1 
## PC_ 4 
## Positive:  CHIC2, PDGFRA, FIP1L1, SRD5A3, TMEM165, SCFD2, CLOCK, DANCR, EXOC1, SGCB 
##     AASDH, DCUN1D4, PPAT, OCIAD1, FRYL, PAICS, NFXL1, SRP72, COMMD8, GNPDA2 
##     NOA1, GUF1, POLR2B, ATP8A1, SLC30A9, LPHN3, TMEM33, UBA6, LIMCH1, UCHL1 
## Negative:  EIF4E, METAP1, TSPAN5, ADH5, RAP1GDS1, LAMTOR3, PDLIM5, SMARCAD1, GRID2, SNCA 
##     FAM13A, NAP1L5, PIGY, HERC3, PYURF, PPM1K, PKD2, SPP1, SPARCL1, NUDT9 
##     HSD17B11, ADD1, TNIP2, MFSD10, RGS12, FAM193A, LRPAP1, RNF4, TMEM128, MXD4 
## PC_ 5 
## Positive:  FAM149A, UFSP2, ANKRD37, KIAA1430, SLC25A4, ACSL1, CASP3, IRF2, STOX2, TRAPPC11 
##     RWDD4, ING2, CDKN2AIP, AGA, SPCS3, GPM6A, GLRA3, CEP44, FBXO8, SCRG1 
##     HMGB2, AADAT, MFAP3L, C4orf27, COX18, DCK, ANKRD17, MOB1B, IL8, GRSF1 
## Negative:  LSM6, SLC10A7, TMEM184C, PRMT10, DCLK2, RPS3A, SH3D19, PET112, FBXW7, ARFIP1 
##     TRIM2, KIAA0922, TLR2, PLRG1, CTSO, PDGFC, GLRB, GRIA2, TMEM144, ETFDH 
##     PPID, RAPGEF2, NAF1, TMA16, LAMTOR3, ADH5, MARCH1, METAP1, EIF4E, FAM218A

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  BOD1, CPEB4, BNIP1, CREBRF, ATP6V0E1, RPL26L1, ERGIC1, DUSP1, FBXW11, NPM1 
##     RANBP17, CCDC127, PANK3, AFF4, SDHA, RARS, LEAP2, MAT2B, UQCRQ, PDCD6 
##     NUDCD2, SEPT8, KIF3A, RAD50, CCNG1, C5orf55, IRF1, GABRG2, C5orf56, EXOC3 
## Negative:  COX7C, EDIL3, HAPLN1, RASA1, VCAN, CCNH, TMEM161B, XRCC4, TMEM161B-AS1, LINC00461 
##     MEF2C, TMEM167A, CETN3, RPS23, MBLAC2, ATG10, COL4A3BP, SSBP2, POLK, HMGCR 
##     ZCCHC9, POC5, ARRDC3, MSH3, MTRNR2L2, FAM169A, F2R, ZFYVE16, AGGF1, PDE8B 
## PC_ 2 
## Positive:  PCDHB13, PCDHB12, PCDHB19P, PCDHB11, TAF7, PCDHB9, PCDHGB2, PCDHB16, PCDHGA7, PCDHB8 
##     PCDHGB4, PCDHB7, PCDHGA10, ZMAT2, PCDHGB7, HARS2, PCDHGC3, PCDHGC4, HARS, HDAC3 
##     PCDH1, KIAA0141, DND1, RNF14, GNPDA1, WDR55, NDFIP1, FGF1, NR3C1, IK 
## Negative:  DHX29, SKIV2L2, ARL15, NDUFS4, PPAP2A, MOCS2, PARP8, MRPS30, SLC38A9, NNT 
##     IL6ST, PAIP1, MIER3, C5orf28, HMGCS1, GPBP1, NIM1, PLK2, ERCC8, ZNF131 
##     NDUFAF2, SMIM15, SEPP1, ZSWIM6, FBXO4, KIF2A, DIMT1, C5orf51, IPO11, OXCT1 
## PC_ 3 
## Positive:  FAM173B, CCT5, SEMA5A, CMBL, FASTKD3, MARCH6, MTRR, DAP, SRD5A1, NSUN2 
##     CTNND2, MED10, NDUFS6, TRIO, MRPL36, FAM105A, SDHAP3, ANKH, LPCAT1, CLPTM1L 
##     ZNF622, BRD9, MYO10, ZDHHC11, TPPP, BASP1, EXOC3, GUSBP1, C5orf55, CDH10 
## Negative:  RASA1, CCNH, COX7C, EDIL3, TMEM161B, HAPLN1, TMEM161B-AS1, RPS23, ATG10, VCAN 
##     XRCC4, TMEM167A, LINC00461, SSBP2, ZCCHC9, MEF2C, MSH3, ERAP1, CETN3, LNPEP 
##     CAST, MBLAC2, ARRDC3, RIOK2, ELL2, MTRNR2L2, FAM172A, GLRX, TTC37, RGMB 
## PC_ 4 
## Positive:  SLC12A2, ISOC1, HINT1, PRRC1, LYRM7, PHAX, ALDH7A1, CDC42SE2, GRAMD3, RAPGEF6 
##     ZNF608, FNIP1, CSNK1G3, ACSL6, SNX24, SLC22A5, SNX2, C5orf56, IRF1, SRFBP1 
##     RAD50, HSD17B4, KIF3A, SEPT8, DMXL1, UQCRQ, SEMA6A, LEAP2, AFF4, COMMD10 
## Negative:  CCNG1, GABRG2, SLU7, PWWP2A, NUDCD2, TTC1, MAT2B, UBLCP1, RNF145, RARS 
##     CLINT1, PANK3, RANBP17, THG1L, NPM1, CYFIP2, FBXW11, MED7, DUSP1, ERGIC1 
##     HAVCR2, RPL26L1, ATP6V0E1, CREBRF, BNIP1, BOD1, CPEB4, DCTN4, RBM22, NDST1 
## PC_ 5 
## Positive:  SMIM15, NDUFAF2, ZSWIM6, ERCC8, PLK2, KIF2A, GPBP1, DIMT1, IPO11, MIER3 
##     RNF180, IL6ST, CWC27, SLC38A9, PPWD1, PPAP2A, TRIM23, SKIV2L2, TRAPPC13, DHX29 
##     SGTB, ARL15, NLN, NDUFS4, DNAJC18, TMEM173, MOCS2, UBE2D2, CXXC5, PARP8 
## Negative:  TTC37, RHOBTB3, FAM172A, GLRX, ARRDC3, ELL2, MBLAC2, CAST, CETN3, ERAP1 
##     MEF2C, LNPEP, LINC00461, RIOK2, TMEM161B-AS1, RGMB, TMEM161B, CHD1, CCNH, FAM174A 
##     NSUN2, MED10, SRD5A1, MRPL36, NDUFS6, SDHAP3, MTRR, LPCAT1, RASA1, FASTKD3

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  BAG2, PRIM2, ZNF451, GUSBP4, KIAA1586, KHDRBS2, BEND6, DST, PTP4A1, PHF3 
##     GCLC, BAI3, ELOVL5, LMBRD1, ICK, FAM135A, GSTA4, C6orf57, SMAP1, TMEM14A 
##     MTO1, EEF1A1, EFHC1, SLC17A5, COX7A2, PAQR8, TMEM30A, SENP6, MYO6, PHIP 
## Negative:  VARS, LSM2, MSH5, CLIC1, HSPA1A, DDAH2, ABHD16A, HSPA1B, LY6G5C, C6orf48 
##     NELFE, SKIV2L, STK19, C2, EHMT2, NEU1, ATF6B, LY6G5B, PPT2, PPT2-EGFL8 
##     EGFL8, CSNK2B, AGPAT1, GPANK1, HLA-DRA, C6orf47, HLA-DRB5, BAG6, HLA-DRB1, PRRC2A 
## PC_ 2 
## Positive:  PRDM1, PREP, ATG5, HACE1, GRIK2, ASCC3, RTN4IP1, CCNC, PNISR, QRSL1 
##     COQ3, FBXL4, C6orf203, POU3F2, PDSS2, KLHL32, SEC63, NDUFAF4, OSTM1, UFL1 
##     SNX3, FOXO3, FUT9, MANEA, SESN1, MAP3K7, CEP57L1, CASP8AP2, CD164, MICAL1 
## Negative:  CAHM, AGPAT4, QKI, MAP3K4, SFT2D1, LPAL2, MPC1, RPS6KA2, MRPL18, RNASET2 
##     TCP1, FGFR1OP, ACAT2, MLLT4, THBS2, WTAP, SOD2, C6orf120, TAGAP, LINC00574 
##     EZR, DLL1, DYNLT1, FAM120B, TMEM181, PSMB1, TULP4, TBP, PDCD2, SERAC1 
## PC_ 3 
## Positive:  PEX7, BCLAF1, AHI1, IFNGR1, TNFAIP3, HBS1L, SGK1, HMGA1P7, KIAA1244, TBPL1 
##     NHSL1, RPS12, CCDC28A, ABRACL, SLC18B1, CITED2, STX7, VTA1, MED23, AIG1 
##     ARG1, PEX3, AKAP7, FUCA2, LTV1, EPB41L2, SF3B5, PTPRK, FBXO30, SHPRH 
## Negative:  GMNN, C6orf62, HIST1H1C, HIST1H4C, ACOT13, ALDH5A1, TDP2, GPLD1, MRS2, NRSN1 
##     HIST1H2BC, SOX4, CDKAL1, HIST1H2AC, MBOAT1, HIST1H1E, DEK, HIST1H2BD, TPMT, HIST1H4E 
##     KIF13A, HIST1H2BG, BTN3A2, NUP153, BTN3A1, BTN3A3, BTN2A1, HMGN4, FAM8A1, ABT1 
## PC_ 4 
## Positive:  NHSL1, CCDC28A, KIAA1244, ABRACL, TNFAIP3, CITED2, IFNGR1, PEX3, VTA1, AIG1 
##     PEX7, FUCA2, BCLAF1, LTV1, AHI1, HBS1L, SF3B5, FBXO30, SGK1, SHPRH 
##     HMGA1P7, TBPL1, SASH1, RPS12, UST, SLC18B1, PHACTR1, NEDD9, TBC1D7, SIRT5 
## Negative:  PPP2R5D, MEA1, CNPY3, KLHDC3, C6orf226, KLC4, RPL7L1, TBCC, UBR2, TRERF1 
##     NFYA, TREM2, MRPS10, TREM1, MED20, BYSL, TAF8, TOMM6, CCND3, OARD1 
##     MOCS1, SAYSD1, GLO1, BTBD9, ZFAND3, CCDC167, RNF8, PIM1, FGD2, CDC5L 
## PC_ 5 
## Positive:  SFT2D1, QKI, MPC1, CAHM, RPS6KA2, AGPAT4, MAP3K4, RNASET2, LPAL2, MRPL18 
##     FGFR1OP, TCP1, ACAT2, MLLT4, TMEM181, WTAP, TULP4, DYNLT1, TAGAP, SOD2 
##     EZR, SERAC1, THBS2, TMEM242, ARID1B, C6orf120, TFB1M, LINC00574, SCAF8, DLL1 
## Negative:  SRSF3, CDKN1A, PPIL1, STK38, C6orf89, KCTD20, MTCH1, FGD2, BRPF3, PIM1 
##     SRPK1, RNF8, FKBP5, CCDC167, ZFAND3, RPL10A, BTBD9, PPARD, GLO1, DEF6 
##     SAYSD1, ZNF76, MOCS1, OARD1, TAF11, NFYA, UHRF1BP1, TREM2, SNRPC, TREM1

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  PDK4, PPP1R9A, DYNC1I1, PON2, PEG10, SLC25A13, SGCE, SHFM1, CASD1, BET1 
##     ACN9, CCDC132, ASNS, FAM133B, LMTK2, RBM48, TECPR1, PEX1, GATAD1, BRI3 
##     ANKIB1, KRIT1, TMEM130, CROT, CYP51A1, TP53TG1, SLC25A40, TMEM243, DBF4, AKAP9 
## Negative:  CUL1, FAM115A, CNTNAP2, EZH2, ZYX, PDIA4, FAM131B, ZNF425, ZNF282, CASP2 
##     GSTK1, ZNF212, MTRNR2L6, ZNF767, SSBP1, KIAA1147, ATP6V0E2, H2AFV, PPIA, TRIL 
##     AGK, MRPS33, ZMIZ2, CREB5, BRAF, OGDH, REPIN1, NDUFB2, JAZF1, TMED4 
## PC_ 2 
## Positive:  SLC25A13, DYNC1I1, SHFM1, PDK4, ACN9, ASNS, LMTK2, PON2, TECPR1, PPP1R9A 
##     BRI3, PEG10, TMEM130, SGCE, ARPC1A, CASD1, ARPC1B, BET1, PDAP1, CCDC132 
##     FAM133B, BUD31, RBM48, PTCD1, PEX1, GATAD1, CPSF4, ANKIB1, ATP5J2, KRIT1 
## Negative:  PHF14, NDUFA4, NXPH1, THSD7A, TMEM106B, ICA1, GLCCI1, SCIN, RPA3, ARL4A 
##     MIOS, C1GALT1, CCZ1B, ETV1, ZDHHC4, KDELR2, DGKB, DAGLB, ANKMY2, RAC1 
##     BZW2, FAM220A, TSPAN13, USP42, SNX13, EIF2AK1, HDAC9, AIMP2, TNPO3, AHCYL2 
## PC_ 3 
## Positive:  FAM220A, USP42, AIMP2, EIF2AK1, CCZ1, PMS2, RNF216, RAC1, FSCN1, DAGLB 
##     ACTB, KDELR2, ZDHHC4, WIPI2, CCZ1B, C1GALT1, RNF216P1, MIOS, MMD2, RPA3 
##     AP5Z1, GLCCI1, FOXK1, ICA1, GNA12, NXPH1, AMZ1, NDUFA4, TTYH3, PHF14 
## Negative:  TMEM140, WDR91, C7orf49, CNOT4, CALD1, NUP205, BPGM, C7orf73, MTPN, AKR1B1 
##     LUZP6, SLC35B4, PTN, EXOC4, DGKI, CHCHD3, CREB3L2, PODXL, TRIM24, MKLN1 
##     ZC3HAV1, COPG2, UBN2, MEST, C7orf55, CEP41, LUC7L2, TMEM209, HIPK2, KLHDC10 
## PC_ 4 
## Positive:  SPDYE8P, STAG3L3, NSUN5, NSUN5P2, POM121, BAZ1B, SPDYE7P, BCL7B, SBDSP1, STAG3L4 
##     PMS2P4, TYW1, SBDS, TMEM248, RABGEF1, KCTD7, LINC00174, TPST1, CRCP, ASL 
##     GUSB, VKORC1L1, CCT6P1, ZNF92, CCT6P3, ERV3-1, ZNF117, ZNF138, ZNF107, ZNF680 
## Negative:  ZSCAN25, TRIM4, ZNF655, ZSCAN21, FAM200A, ZKSCAN5, AZGP1, ZKSCAN1, ZNF3, ZNF394 
##     COPS6, ZNF789, MCM7, AP4M1, ATP5J2, TAF6, CNPY4, CPSF4, LAMTOR4, PTCD1 
##     GAL3ST4, BUD31, GPC2, PDAP1, ARPC1B, GATS, ARPC1A, PVRIG, PMS2P1, TMEM130 
## PC_ 5 
## Positive:  GNAI1, MAGI2-AS3, MAGI2, CACNA2D1, PHTF2, GRM3, TMEM60, DMTF1, RSBN1L, RSBN1L-AS1 
##     TMEM243, PTPN12, TP53TG1, POMZP3, CROT, DTX2, SLC25A40, DBF4, YWHAG, ADAM22 
##     HSPB1, MDH2, SRI, STYXL1, STEAP2, CLDN12, MTERF, AKAP9, ARF5, GCC1 
## Negative:  PRKAG2, NUB1, RHEB, GALNT11, ABCF2, PAXIP1, DPP6, INSIG1, AGAP3, RBM33 
##     TMUB1, LMBR1, FASTK, DNAJB6, PTPRN2, CDK5, ESYT2, ABCB8, WDR60, LINC00689 
##     KCNH2, VIPR2, TMEM176B, GIMAP2, GIMAP4, REPIN1, ATP6V0E2, ZNF767, ZNF212, ZNF282

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  JRK, ARC, TSNARE1, DENND3, PTK2, CHRAC1, TRAPPC9, KHDRBS3, NDRG1, SLA 
##     PHF20L1, EFR3A, ASAP1, FAM49B, MYC, FAM84B, TRIB1, NSMCE2, KIAA0196, SQLE 
##     MTSS1, NDUFB9, TATDN1, RNF139, TRMT12, DECR1, NBN, RIPK2, TMEM55A, FAM91A1 
## Negative:  BNIP3L, PPP2R2A, PNMA2, ADAM28, SLC25A37, DPYSL2, ENTPD4, R3HCC1, CHMP7, ADRA1A 
##     TNFRSF10B, RHOBTB2, EGR3, STMN4, BIN3, TRIM35, PDLIM2, PTK2B, SORBS3, CLU 
##     PPP3CC, SCARA3, SLC39A14, CCDC25, POLR3D, ELP3, REEP4, FZD3, FAM160B2, XPO7 
## PC_ 2 
## Positive:  CPNE3, REXO1L1, MMP16, CA2, RIPK2, C8orf59, NBN, ZFAND1, DECR1, IMPA1 
##     TMEM55A, PMP2, OTUD6B, FABP5, RUNX1T1, PAG1, TRIQK, ZNF704, FAM92A1, TPD52 
##     MRPS28, RBM12B, HEY1, STMN2, PDP1, ZC2HC1A, KIAA1429, DPY19L4, INTS8, CCNE2 
## Negative:  CLN8, ERICH1, FBXO25, CSMD1, ZNF596, MCPH1, AGPAT5, ERI1, TNKS, MSRA 
##     PINX1, CTSB, MTMR9, ZDHHC2, MSR1, NEIL2, FDFT1, TUSC3, CNOT7, VPS37A 
##     MTMR7, MTUS1, PCM1, ASAH1, PSD3, CSGALNACT1, INTS10, LPL, ATP6V1B2, XPO7 
## PC_ 3 
## Positive:  PPAPDC1B, WHSC1L1, FGFR1, DDHD2, RNF5P1, BAG4, LSM1, ASH2L, BRF2, EIF4EBP1 
##     PROSC, DUSP26, ERLIN2, UBE2V2, RPS20, RNF122, TGS1, CHCHD7, PCMTD1, TMEM68 
##     MAK16, MRPL15, TTI2, RB1CC1, IMPAD1, LYPLA1, FUT10, ATP6V1H, TCEA1, FAM110B 
## Negative:  NSMCE2, KIAA0196, TRIB1, SQLE, FAM84B, MTSS1, NDUFB9, MYC, TATDN1, FAM49B 
##     RNF139, ASAP1, TRMT12, EFR3A, FAM91A1, WDYHV1, PHF20L1, ZHX1, SLA, C8orf76 
##     NDRG1, DERL1, KHDRBS3, ZHX2, TRAPPC9, CHRAC1, PTK2, DENND3, TSNARE1, ARC 
## PC_ 4 
## Positive:  CPNE3, MMP16, REXO1L1, RIPK2, NBN, CA2, DECR1, C8orf59, TMEM55A, ZFAND1 
##     OTUD6B, IMPA1, RUNX1T1, PMP2, CTSB, TRIQK, TUSC3, FDFT1, FABP5, NEIL2 
##     MSR1, ZDHHC2, MTMR9, PINX1, FAM92A1, CNOT7, PAG1, MSRA, TNKS, RBM12B 
## Negative:  RNF5P1, FGFR1, WHSC1L1, PPAPDC1B, DDHD2, BAG4, LSM1, ASH2L, EIF4EBP1, BRF2 
##     PROSC, ERLIN2, DUSP26, RNF122, MAK16, TTI2, FUT10, PPP2CB, UBE2V2, UBXN8 
##     PCMTD1, GSR, RB1CC1, SMIM18, ATP6V1H, DCTN6, TCEA1, LYPLA1, LEPROTL1, MRPL15 
## PC_ 5 
## Positive:  FZD3, EXTL3, ELP3, INTS9, CCDC25, SCARA3, CLU, HMBOX1, PTK2B, KIF13B 
##     TRIM35, TMEM66, STMN4, LEPROTL1, ADRA1A, DCTN6, DPYSL2, SMIM18, PNMA2, GSR 
##     BNIP3L, UBXN8, PPP2R2A, PPP2CB, ADAM28, FUT10, PTDSS1, CPQ, MTERFD1, UQCRB 
## Negative:  SDCBP, UBXN2B, NSMAF, FAM110B, IMPAD1, TOX, CHCHD7, CA8, RPS20, RAB2A 
##     TGS1, CHD7, TMEM68, CLVS1, MRPL15, LYPLA1, TCEA1, ATP6V1H, RB1CC1, PCMTD1 
##     UBE2V2, ZNF596, FBXO25, ERICH1, CLN8, CSMD1, MCPH1, AGPAT5, ERI1, TNKS

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  GPSM1, PMPCA, NACC2, UBAC1, SEC16A, CAMSAP1, NOTCH1, MRPS2, PPP1R26, OLFM1 
##     SNHG7, TMEM141, WDR5, PHPT1, BRD3, EDF1, TRAF2, LINC00094, FBXW5, PTGDS 
##     VAV2, ADAMTSL2, SLC2A6, REXO4, CACFD1, SURF4, SURF2, SURF1, RPL7A, MED22 
## Negative:  TBC1D2, TRIM14, TGFBR1, NANS, ALG2, ANP32B, C9orf156, SEC61B, XPA, NCBP1 
##     NR4A3, TSTD2, TMOD1, ZNF510, STX17, CDC14B, ERCC6L2, ERP44, LINC00476, PTCH1 
##     INVS, C9orf3, TEX10, HIATL1, MSANTD3, PHF2, MSANTD3-TMEFF1, FAM120A, LPPR1, MRPL50 
## PC_ 2 
## Positive:  B4GALT1, SMU1, BAG1, DNAJA1, CHMP5, APTX, NFX1, NDUFB6, NOL6, TOPORS 
##     UBE2R2, DDX58, UBAP2, ACO1, DCAF12, C9orf72, UBAP1, MOB3B, NUDT2, IFT74 
##     KIAA1161, PLAA, FAM219A, CAAP1, RPP25L, CDKN2A, DCTN3, SIGMAR1, MTAP, GALT 
## Negative:  ASTN2, TRIM32, ATP6V1G1, POLE3, CDK5RAP2, ALAD, MEGF9, PRPF4, CDC26, SLC31A1 
##     FKBP15, SLC31A2, PSMD5, ZFP37, SNX30, ZNF883, INIP, HSDL2, PTBP3, UGCG 
##     RAB14, GNG10, ZNF483, GSN, KIAA0368, LPAR1, TXN, TMEM245, CTNNAL1, NDUFA8 
## PC_ 3 
## Positive:  SURF1, RPL7A, SURF2, SURF4, MED22, REXO4, SURF6, CACFD1, GBGT1, SLC2A6 
##     ADAMTSL2, RALGDS, VAV2, GTF3C5, LINC00094, TSC1, BRD3, WDR5, C9orf9, OLFM1 
##     TTF1, PPP1R26, MRPS2, SETX, CAMSAP1, UBAC1, MED27, NACC2, UCK1, GPSM1 
## Negative:  C9orf156, XPA, ANP32B, NCBP1, TSTD2, TMOD1, ZNF510, NANS, CDC14B, ERCC6L2 
##     LINC00476, TRIM14, PTCH1, C9orf3, TBC1D2, HIATL1, PHF2, TGFBR1, FAM120A, ALG2 
##     FAM120AOS, SEC61B, NR4A3, NINJ1, STX17, SUSD3, ERP44, FGD3, INVS, TEX10 
## PC_ 4 
## Positive:  RANBP6, IL33, KIAA2026, UHRF2, PLGRKT, KDM4C, JAK2, PTPRD, MPDZ, RCL1 
##     NFIB, AK3, ZDHHC21, CDC37L1, PPAPDC2, SNAPC3, RFX3, PSIP1, KIAA0020, SMARCA2 
##     CNTLN, KANK1, RRAGA, DOCK8, HAUS6, CBWD1, PLIN2, DENND4C, RPS6, SLC24A2 
## Negative:  FAM122A, CBWD3, FXN, CBWD5, APBA1, SMC5, C9orf85, CBWD6, ZFAND5, NMRK1 
##     PGM5P2, OSTF1, RFK, PRUNE2, IGFBPL1, GNAQ, CEP78, ALDH1B1, PSAT1, SLC25A51 
##     IDNK, UBQLN1, EXOSC3, HNRNPK, RMI1, TRMT10B, NTRK2, TOMM5, AGTPBP1, FBXO10 
## PC_ 5 
## Positive:  ARPC5L, GOLGA1, RPL35, SCAI, PPP6C, MIR181A2HG, RABEPK, PSMB7, HSPA5, NEK6 
##     DENND1A, RABGAP1, ZBTB26, ZBTB6, RC3H2, PDCL, MRRF, RBM18, NDUFA8, GSN 
##     RAB14, PSMD5, MEGF9, CDK5RAP2, TRIM32, CCDC107, TLN1, RUSC2, CREB3, ASTN2 
## Negative:  CBWD1, DOCK8, KANK1, SMARCA2, KIAA0020, RFX3, PPAPDC2, CDC37L1, AK3, RCL1 
##     JAK2, PLGRKT, KIAA2026, RANBP6, IL33, BICD2, ZNF484, UHRF2, IPPK, FGD3 
##     NOL8, SUSD3, NINJ1, IARS, FAM120AOS, KDM4C, FAM120A, SPTLC1, PHF2, AUH

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  MTG1, ECHS1, ZNF511, TUBGCP2, INPP5A, LRRC27, DPYSL4, BNIP3, PPP2R2D, GLRX3 
##     CDC123, PTPRE, CAMK1D, SEPHS1, DOCK1, PRPF18, FRMD4A, C10orf90, FAM107B, HSPA14 
##     BCCIP, SUV39H2, DCLRE1C, UROS, RPP38, NMT2, FAM171A1, C10orf137, FAM188A, RSU1 
## Negative:  SLC29A3, PCBD1, PALD1, EIF4EBP2, SGPL1, C10orf54, PPA1, SAR1A, PSAP, TYSND1 
##     CHST3, TSPAN15, ASCC1, ANAPC16, HK1, DDIT4, SUPV3L1, DNAJB12, VPS26A, MICU1 
##     MCU, SRGN, P4HA1, KIAA1279, ECD, DDX21, DNAJC9, DDX50, MRPS16, ANXA7 
## PC_ 2 
## Positive:  HNRNPF, ZNF239, CSGALNACT2, BMS1, ZNF485, ZNF33B, ZNF37BP, HSD17B7P2, ZNF37A, ZNF33A 
##     ZNF32, ZNF25, ZNF248, CXCL12, CCNY, RASSF4, CREM, ZNF22, CUL2, ALOX5 
##     FAM21C, NRP1, AGAP4, ITGB1, BMS1P1, EPC1, GLUD1P7, KIF5B, ARHGAP12, BMS1P2 
## Negative:  CCSER2, RGR, GRID1, CDHR1, WAPAL, GHITM, BMPR1A, GLUD1, TSPAN14, FAM213A 
##     FAM35A, TMEM254, MINPP1, ZCCHC24, ATAD1, PPIF, PTEN, ZMIZ1, RPS24, STAMBPL1 
##     POLR3A, ACTA2, DLG5, KCNMA1, FAS, VDAC2, CH25H, LIPA, SAMD8, IFIT2 
## PC_ 3 
## Positive:  MCU, MICU1, DNAJB12, P4HA1, ECD, DDIT4, DNAJC9, MRPS16, ANAPC16, ANXA7 
##     MTRNR2L5, PCDH15, PPP3CB, ZWINT, CSTF2T, ASCC1, CISD1, SGMS1, USP54, BMS1P4 
##     FAM21A, AGAP5, SEC24C, FUT11, UBE2D1, KAT6B, AGAP6, CHCHD1, CHST3, SAMD8 
## Negative:  GSTO1, SFR1, ITPRIP, XPNPEP1, PDCD11, ADD3, MXI1, USMG5, SMNDC1, SMC3 
##     PCGF6, PDCD4, INA, NT5C2, BBIP1, AS3MT, SHOC2, ZDHHC6, C10orf32, VTI1A 
##     WBP1L, TCF7L2, SFXN2, DCLRE1A, ARL3, NHLRC2, FAM160B1, TRIM8, TRUB1, ACTR1A 
## PC_ 4 
## Positive:  CHST15, BUB3, OAT, ACADSB, LHPP, IKZF5, FAM53B, METTL10, PSTK, C10orf88 
##     FAM175B, HTRA1, CTBP2, PLEKHA1, C10orf137, TACC2, UROS, NSMCE4A, BCCIP, ATE1 
##     C10orf90, WDR11, DOCK1, PTPRE, PPAPDC1A, GLRX3, SEC23IP, PPP2R2D, BNIP3, MCMBP 
## Negative:  SEC31B, LINC00263, SCD, NDUFB8, BLOC1S2, CWF19L1, HIF1AN, CHUK, ERLIN1, FAM178A 
##     DNMBP, COX15, MRPL43, CUTC, SLC25A28, LZTS2, GOT1, SFXN3, HPS1, BTRC 
##     R3HCC1L, CRTAC1, ZFYVE27, AVPI1, MORN4, MMS19, ZDHHC16, LDB1, EXOSC1, PPRC1 
## PC_ 5 
## Positive:  OTUD1, MSRB2, ARHGAP21, PIP4K2A, PRTFDC1, COMMD3-BMI1, COMMD3, THNSL1, DNAJC1, NEBL 
##     PLXDC2, GPR158, ARL5B, NSUN6, STAM, APBB1IP, RSU1, FAM188A, FAM171A1, PDSS1 
##     NMT2, RPP38, ABI1, DCLRE1C, ANKRD26, SUV39H2, HSPA14, YME1L1, FAM107B, ACBD5 
## Negative:  DNAJC12, SIRT1, LRRTM3, HERC4, CTNNA3, PBLD, HNRNPH3, RUFY2, REEP3, SLC25A16 
##     JMJD1C, TET1, NRBF2, CCAR1, EGR2, DDX50, ZNF365, DDX21, ARID5B, KIAA1279 
##     ANK3, SRGN, CCDC6, VPS26A, FAM13C, PHYHIPL, SUPV3L1, TFAM, HK1, UBE2D1

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  MRPL48, COA4, RAB6A, PLEKHB1, STARD10, FAM168A, ATG16L2, PAAF1, RELT, FCHSD2 
##     UCP2, C2CD3, PPME1, PGM2L1, POLD3, XRRA1, SPCS2, SLCO2B1, RPS3, B3GAT1 
##     ACAD8, THYN1, VPS26B, NCAPD3, JAM3, IGSF9B, NTM, SNX19, ZBTB44, PHRF1 
## Negative:  CD82, EXT2, ALKBH3, TP53I11, SLC35C1, CRY2, HSD17B12, MAPK8IP1, PEX16, PHF21A 
##     TTC17, MDK, AMBRA1, HARBI1, API5, ATG13, LRRC4C, ARHGAP1, C11orf74, ZNF408 
##     TRAF6, CKAP5, COMMD9, LRP4, LDLRAD3, TRIM44, C11orf49, SLC1A2, APIP, PDHX 
## PC_ 2 
## Positive:  VWA5A, ZNF202, TBRG1, SIAE, HEPACAM, SCN3B, GRAMD1B, HEPN1, HSPA8, SLC37A2 
##     SORL1, FEZ1, TMEM136, EI24, PVRL1, STT3A, PUS3, THY1, DDX25, USP2 
##     RPUSD4, RNF26, FAM118B, SRPR, MCAM, FOXRED1, CBL, TIRAP, DCPS, HINFP 
## Negative:  SVIP, FANCF, LUZP2, PRMT3, FIBIN, LIN7C, HTATIP2, BDNF-AS, NAV2-AS5, NAV2 
##     ZDHHC13, COPB1, METTL15, PSMA1, FAR1, TMEM86A, CYP2R1, SPTY2D1, SOX6, BTBD10 
##     UEVLD, ARL14EP, C11orf58, TSG101, RPS13, PIK3C2A, NUCB2, LDHA, MPPED2, GTF2H1 
## PC_ 3 
## Positive:  ABCC8, SERGEF, NUCB2, SAAL1, PIK3C2A, HPS5, RPS13, GTF2H1, C11orf58, LDHA 
##     TSG101, SOX6, UEVLD, CYP2R1, SPTY2D1, TMEM86A, ZDHHC13, PSMA1, NAV2, COPB1 
##     NAV2-AS5, FAR1, HTATIP2, BTBD10, ARNTL, PRMT3, TEAD1, FANCF, PARVA, SVIP 
## Negative:  PICALM, EED, C11orf73, ME3, TMEM135, CTSC, CHORDC1, SLC36A4, TAF1D, C11orf54 
##     MED17, PANX1, ANKRD49, CWC15, SRSF8, RPS3, ENDOD1, FAM76B, SLCO2B1, CEP57 
##     SPCS2, MTMR2, MAML2, XRRA1, CCDC82, POLD3, JRKL, PGM2L1, BIRC2, PPME1 
## PC_ 4 
## Positive:  FADS1, BEST1, FTH1, FADS2, ASRGL1, FEN1, EEF1G, TUT1, TMEM258, MTA2 
##     MYRF, B3GAT3, GANAB, INTS5, C11orf48, SDHAF2, C11orf83, CPSF7, UBXN1, TMEM216 
##     BSCL2, TMEM138, TTC9C, DAK, ZBTB3, POLR2G, TAF6L, TMEM223, TMEM179B, NXF1 
## Negative:  ACAT1, NPAT, CUL5, SLC35F2, ELMOD1, ATM, CWF19L2, DDX10, AASDHPPT, RDX 
##     MSANTD4, FDX1, GRIA4, CASP1, LAYN, CASP4, SIK2, TMEM123, PPP2R1B, BIRC2 
##     JRKL, ALG9, CCDC82, C11orf1, MAML2, CRYAB, MTMR2, CEP57, DIXDC1, FAM76B 
## PC_ 5 
## Positive:  CARS, OSBPL5, NAP1L4, ZNF195, NUP98, PGAP2, KCNQ1OT1, RHOG, TSSC4, STIM1 
##     CD81, RRM1, MRPL23, TRIM68, CTSD, TRIM22, IFITM10, MOB2, FAM160A2, TOLLIP 
##     SMPD1, CHID1, POLR2L, APBB1, CD151, TRIM3, PNPLA2, RPLP2, ARFIP2, PIDD 
## Negative:  TTC17, ALKBH3, HSD17B12, API5, EXT2, CD82, TP53I11, LRRC4C, SLC35C1, C11orf74 
##     CRY2, TRAF6, MAPK8IP1, PEX16, COMMD9, PHF21A, MDK, LDLRAD3, AMBRA1, TRIM44 
##     HARBI1, ATG13, SLC1A2, ARHGAP1, ZNF408, PDHX, CKAP5, LRP4, APIP, C11orf49

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  KDM5A, NINJ2, WNK1, RAD52, ZCCHC8, ERC1, CLIP1, ADIPOR2, VPS33A, DCP1B 
##     DIABLO, FKBP4, MLXIP, ITFG2, NRIP2, BCL7A, RHNO1, PSMD9, TULP3, KDM2B 
##     PARP11, RNF34, CCND2, ANAPC5, C12orf5, CAMKK2, C12orf4, P2RX4, DYRK4, P2RX7 
## Negative:  GLIPR1, KRR1, PHLDA1, NAP1L1, GLIPR1L2, ATXN7L3B, BBS10, TBC1D15, RAB21, OSBPL8 
##     TMEM19, ALKBH2, SVOP, USP30, ZDHHC17, THAP2, UNG, KCTD10, UBE3B, SSH1 
##     PPP1R12A, MMAB, ZFC3H1, PPFIA2, CCDC59, MVK, CORO1C, LGR5, C12orf29, SELPLG 
## PC_ 2 
## Positive:  CLSTN3, PEX5, SLC2A3, TMEM19, THAP2, CNOT2, ZFC3H1, LGR5, C3AR1, RAB21 
##     RAB3IP, NECAP1, TBC1D15, CCT2, ATXN7L3B, CLEC4A, FRS2, GLIPR1L2, FAM66C, GLIPR1 
##     YEATS4, RIMKLB, KRR1, LYZ, PHC1, PHLDA1, PTMS, NAP1L1, CPSF6, M6PR 
## Negative:  WSB2, RFC5, VSIG10, FBXO21, PEBP1, FBXW8, TAOK3, RNFT2, MAP1LC3B2, SUDS3 
##     MED13L, PRKAB1, CIT, GCN1L1, PLBD2, RPLP0, PXN-AS1, TPCN1, C12orf52, PXN 
##     DDX54, COX6A1, RASAL1, TRIAP1, OAS1, GATC, SRSF9, RPH3A, DYNLL1, PTPN11 
## PC_ 3 
## Positive:  CHST11, SLC41A2, C12orf45, TXNRD1, ALDH1L2, KIAA1033, NFYB, HCFC2, APPL2, TDG 
##     C12orf75, C12orf73, HSP90B1, CKAP4, NT5DC3, TCP11L2, ASCL1, POLR3B, RIC8B, NUP37 
##     C12orf23, MTERFD3, CCDC53, CRY1, PWP1, GNPTAB, CMKLR1, FICD, ARL1, SART3 
## Negative:  MRPL51, GAPDH, TAPBPL, VAMP1, CD27-AS1, TNFRSF1A, IFFO1, CD9, NOP2, NDUFA9 
##     DYRK4, CHD4, C12orf4, LPAR5, C12orf5, CCND2, ING4, PARP11, ZNF384, TULP3 
##     RHNO1, COPS7A, NRIP2, MLF2, ITFG2, FKBP4, PTMS, DCP1B, ADIPOR2, ERC1 
## PC_ 4 
## Positive:  CTDSP2, TSFM, USP15, METTL1, CDK4, MON2, TSPAN31, PPM1H, OS9, B4GALNT1 
##     DTX3, TMEM5, PIP4K2C, SRGAP1, KIF5A, C12orf66, DCTN2, XPOT, TBK1, DDIT3 
##     GNS, MARS, LEMD3, LLPH, ARHGAP9, TMBIM4, R3HDM2, CAND1, SHMT2, DYRK2 
## Negative:  MTERFD3, C12orf23, CRY1, RIC8B, PWP1, POLR3B, CMKLR1, TCP11L2, FICD, CKAP4 
##     SART3, C12orf75, ISCU, TMEM119, APPL2, SELPLG, CORO1C, KIAA1033, SSH1, ALDH1L2 
##     SVOP, C12orf45, USP30, SLC41A2, ALKBH2, CHST11, UNG, TXNRD1, KCTD10, NFYB 
## PC_ 5 
## Positive:  KIAA1467, HEBP1, DDX47, CDKN1B, GPR19, CREBL2, DUSP16, LOH12CR1, LOH12CR2, MANSC1 
##     UBE2N, LRP6, MRPL42, EEA1, BTG1, CRADD, ATP2B1, CCDC41, POC1B, MAGOHB 
##     TMCC3, DUSP6, C12orf29, NDUFA12, KLRC2, CCDC59, NR2C1, PPFIA2, KLRC3, PPP1R12A 
## Negative:  R3HDM2, ARHGAP9, SHMT2, LRP1, MARS, SNORA48, PRIM1, DDIT3, NACA, RAD52 
##     WNK1, NINJ2, DCTN2, KDM5A, ERC1, ADIPOR2, KIF5A, DCP1B, PIP4K2C, FKBP4 
##     DTX3, ITFG2, B4GALNT1, NRIP2, OS9, RHNO1, TSPAN31, TULP3, PARP11, CDK4

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  DZIP1, ABCC4, DNAJC3, TGDS, SNORD22, UGGT2, SLITRK1, MBNL2, SPRY2, RAP2A 
##     NDFIP2, RBM26, IPO5, RNF219, DOCK9, EDNRB, UBAC2, SLAIN1, GPR183, MYCBP2 
##     TM9SF2, FBXL3, PCCA, CLN5, TMTC4, KCTD12, NALCN, UCHL3, COMMD6, FGF14 
## Negative:  FRY, N4BP2L1, N4BP2L2, PDS5B, RFC3, NBEA, SPG20, SMAD9, ALG5, EXOSC8 
##     SUPT20H, UFM1, PROSER1, NHLRC3, LHFP, COG6, MRPS31, ELF1, WBP4, KBTBD6 
##     KBTBD7, NAA16, RGCC, AKAP11, DNAJC15, ENOX1, ING1, CARKD, RAB20, IRS2 
## PC_ 2 
## Positive:  ALG5, SMAD9, SPG20, EXOSC8, NBEA, SUPT20H, RFC3, PDS5B, UFM1, N4BP2L2 
##     PROSER1, N4BP2L1, NHLRC3, FRY, LHFP, COG6, MRPS31, ELF1, WBP4, KBTBD6 
##     KBTBD7, NAA16, RGCC, AKAP11, DNAJC15, ENOX1, MRPS31P5, VPS36, CKAP2, HNRNPA1L2 
## Negative:  ABCC4, DZIP1, TGDS, DNAJC3, SNORD22, UGGT2, SLITRK1, MBNL2, RAP2A, SPRY2 
##     IPO5, NDFIP2, DOCK9, UBAC2, RBM26, GPR183, TM9SF2, RNF219, PCCA, TMTC4 
##     NALCN, FGF14, EDNRB, TPP2, TEX30, KDELC1, SLAIN1, BIVM, ERCC5, MYCBP2 
## PC_ 3 
## Positive:  MRPS31P5, VPS36, CKAP2, HNRNPA1L2, SUGT1, PCDH17, TDRD3, PCDH9, MZT1, DIS3 
##     PIBF1, KLF12, COMMD6, UCHL3, KCTD12, CLN5, FBXL3, MYCBP2, SLAIN1, EDNRB 
##     RNF219, RBM26, ENOX1, NDFIP2, DNAJC15, AKAP11, SPRY2, RGCC, SLITRK1, NAA16 
## Negative:  ING1, CARKD, RAB20, IRS2, MYO16, ABHD13, LIG4, ARGLU1, ERCC5, BIVM 
##     KDELC1, TEX30, TPP2, FGF14, NALCN, TMTC4, PCCA, TM9SF2, GPR183, UBAC2 
##     DOCK9, IPO5, FRY, N4BP2L1, N4BP2L2, PDS5B, RAP2A, RFC3, NBEA, SPG20 
## PC_ 4 
## Positive:  FRY, N4BP2L1, N4BP2L2, PDS5B, RFC3, NBEA, SPG20, SMAD9, ALG5, SPRY2 
##     SLITRK1, NDFIP2, SNORD22, RBM26, TGDS, ABCC4, RNF219, DZIP1, DNAJC3, EDNRB 
##     UGGT2, SLAIN1, EXOSC8, MBNL2, MYCBP2, RAP2A, FBXL3, IPO5, CLN5, SUPT20H 
## Negative:  ENOX1, DNAJC15, AKAP11, RGCC, NAA16, KBTBD7, ING1, KBTBD6, CARKD, RAB20 
##     MRPS31P5, WBP4, IRS2, VPS36, MYO16, ABHD13, ELF1, CKAP2, LIG4, HNRNPA1L2 
##     ARGLU1, MRPS31, SUGT1, ERCC5, BIVM, COG6, PCDH17, KDELC1, TDRD3, TEX30 
## PC_ 5 
## Positive:  ING1, FRY, CARKD, N4BP2L1, RAB20, N4BP2L2, IRS2, VPS36, MRPS31P5, CKAP2 
##     HNRNPA1L2, MYO16, SUGT1, PDS5B, PCDH17, TDRD3, ABHD13, PCDH9, RFC3, MZT1 
##     LIG4, DIS3, NBEA, ARGLU1, PIBF1, SPG20, ERCC5, KLF12, SMAD9, BIVM 
## Negative:  DZIP1, ABCC4, DNAJC3, TGDS, UGGT2, SNORD22, MBNL2, NAA16, SLITRK1, RGCC 
##     KBTBD7, RAP2A, AKAP11, SPRY2, KBTBD6, IPO5, DNAJC15, NDFIP2, WBP4, DOCK9 
##     ENOX1, RBM26, UBAC2, ELF1, GPR183, RNF219, MRPS31, TM9SF2, COG6, EDNRB

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  METTL17, NDRG2, ARHGEF40, ZNF219, HNRNPC, SUPT16H, CHD8, RAB2B, TOX4, METTL3 
##     SALL2, DAD1, ABHD4, OXA1L, MRPL52, LRP10, RBM23, PRMT5, HAUS4, PSMB5 
##     ACIN1, C14orf119, PPP1R3E, C14orf80, BCL2L2-PABPN1, CRIP2, SLC22A17, PACS2, EFS, BRF1 
## Negative:  SLC39A9, ERH, SMOC1, SRSF5, KIAA0247, EXD2, COX16, DCAF5, ZFP36L1, SYNJ2BP 
##     ZFYVE26, MED6, RDH11, PCNX, ZFYVE1, VTI1B, RBM25, PIGH, PSEN1, PLEKHH1 
##     NUMB, ACOT2, PNMA1, EIF2S1, ELMSAN1, PTGR2, ATP6V1D, ZNF410, MPP5, FAM161B 
## PC_ 2 
## Positive:  TMX1, TRIM9, GNG2, PYGL, C14orf166, TXNDC16, NIN, PSMC6, ATL1, STYX 
##     MAP4K5, GNPNAT1, ATP5S, FERMT2, L2HGDH, DDHD1, ARF6, GMFB, NEMF, KLHDC2 
##     KLHDC1, RPL36AL, MGAT2, DNAAF2, RPS29, CGRRF1, MDGA2, SOCS4, MIS18BP1, MAPK1IP1L 
## Negative:  SPATA7, ZC3H14, TTC8, GALC, FOXN3, SEL1L, EFCAB11, DIO2, PSMC1, NRXN3 
##     CALM1, ADCK1, RPS6KA5, SNW1, C14orf159, SLIRP, SMEK1, TRIP11, ALKBH1, NDUFB1 
##     SPTLC2, CPSF2, LGMN, AHSA1, GOLGA5, CHGA, VIPAS39, ITPK1, MOAP1, TMED8 
## PC_ 3 
## Positive:  LINC00643, PPP2R5E, SNAPC1, WDR89, HIF1A, SYNE2, SLC38A6, TRMT5, MTHFD1, MNAT1 
##     ZBTB25, PPM1A, ZBTB1, DHRS7, HSPA2, PCNXL4, PLEKHG3, CHURC1, RTN1, CHURC1-FNTB 
##     FNTB, MAX, JKAMP, FUT8, L3HYPDH, GPHN, KIAA0586, MPP5, ATP6V1D, TIMM9 
## Negative:  MYH7, AP1G2, NGDN, THTPA, JPH4, CMTM5, EFS, DHRS4-AS1, DHRS4, SLC22A17 
##     DHRS4L2, DCAF11, BCL2L2-PABPN1, PSME1, PPP1R3E, EMC9, C14orf119, PSME2, IRF9, ACIN1 
##     REC8, PSMB5, IPO4, HAUS4, TM9SF1, PRMT5, CHMP4A, RBM23, MDP1, LRP10 
## PC_ 4 
## Positive:  PSEN1, NUMB, RBM25, ACOT2, ZFYVE1, PCNX, PNMA1, MED6, ELMSAN1, SYNJ2BP 
##     PTGR2, COX16, ZNF410, SMOC1, SRSF5, FAM161B, KIAA0247, COQ6, SLC39A9, ALDH6A1 
##     LIN52, ERH, ABCD4, EXD2, NPC2, DCAF5, ISCA2, ZFP36L1, FCF1, YLPM1 
## Negative:  SLC25A29, WARS, YY1, WDR25, MEG3, DYNC1H1, PPP2R5C, EVL, HSP90AA1, EML1 
##     WDR20, CINP, CYP46A1, TECPR2, CCNK, CDC42BPB, EIF5, SETD3, MARK3, CKB 
##     VRK1, TRMT61A, BAG5, PAPOLA, KLC1, APOPT1, INF2, C14orf2, ZFYVE21, GSKIP 
## PC_ 5 
## Positive:  C14orf2, INF2, SIVA1, AKT1, ZFYVE21, PLD4, APOPT1, CDCA4, KLC1, BRF1 
##     PACS2, CRIP2, C14orf80, BAG5, TRMT61A, CKB, MARK3, EIF5, CDC42BPB, TECPR2 
##     CINP, ZBTB1, HSPA2, ZBTB25, PLEKHG3, WDR20, MTHFD1, CHURC1, SYNE2, CHURC1-FNTB 
## Negative:  MBIP, LINC00639, BRMS1L, SEC23A, RALGAPA1, GEMIN2, TRAPPC6B, NFKBIA, PNN, CTAGE5 
##     PSMA6, KLHL28, KIAA0391, FAM179B, PRPF39, PPP2R3C, FKBP3, FAM177A1, AHSA1, SPTLC2 
##     VIPAS39, TMED8, ALKBH1, MIS18BP1, GSTZ1, SLIRP, SNW1, POMT2, ADCK1, SRP54

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  UBL7, SEMA7A, CLK3, PML, EDC3, STOML1, CSK, CD276, ULK3, NPTN 
##     NEO1, ADPGK, BBS4, ARIH1, HEXA, PARP6, PKM, SENP8, MYO9A, THAP10 
##     LRRC49, LARP6, TLE3, RPLP1, ANP32A, CORO2B, FEM1B, CLN6, PIAS1, MAP2K5 
## Negative:  RPAP1, TYRO3, VPS18, MGA, RTF1, ZFYVE19, CHP1, OIP5-AS1, NDUFAF1, MAPKBP1 
##     DNAJC17, JMJD7, PLA2G4B, RMDN3, EHD4, VPS39, RPUSD2, TMEM87A, GANC, CAPN3 
##     C15orf57, SNAP23, LRRC57, HAUS2, IVD, UBR1, TMEM62, CCNDBP1, KNSTRN, LCMT2 
## PC_ 2 
## Positive:  OR4M2, TUBGCP5, CYFIP1, NIPA2, HERC2P2, HERC2P7, MKRN3, NDN, SNRPN, SNURF 
##     UBE3A, GABRB3, HERC2, HERC2P9, APBA2, TJP1, FAN1, MTMR10, SCG5, KNSTRN 
##     IVD, C15orf52, PLCB2, C15orf57, EMC7, SRP14, RPUSD2, FAM98B, RMDN3, DNAJC17 
## Negative:  AKAP13, ZNF592, SEC11A, KLHL25, NMB, WDR73, NTRK3, ZSCAN2, MRPL46, UBE2Q2P1 
##     MRPS11, DET1, SH3GL3, AEN, HDGFRP3, MFGE8, TM6SF1, ABHD2, BTBD1, POLG 
##     C15orf40, PEX11A, FAM103A1, AP3S2, WHAMM, C15orf38-AP3S2, C15orf38, CPEB1, IDH2, RPS17L 
## PC_ 3 
## Positive:  NGRN, CRTC3, CIB1, IDH2, MAN2A2, UNC45A, HDDC3, C15orf38, VPS33B, CHD2 
##     RGMA, IGF1R, C15orf38-AP3S2, LRRC28, AP3S2, MEF2A, PEX11A, LINS, POLG, ASB7 
##     VIMP, ABHD2, SNRPA1, MFGE8, PCSK6, TM2D3, TARSL2, AEN, WASH3P, DET1 
## Negative:  MAP2K5, FEM1B, C15orf61, CLN6, PIAS1, AAGAB, CORO2B, RPL4, ANP32A, SNAPC5 
##     MAP2K1, RPLP1, TIPIN, DIS3L, MEGF11, TLE3, RAB11A, LARP6, DENND4A, VWA9 
##     LRRC49, PTPLAD1, DPP8, THAP10, PARP16, MYO9A, CLPX, SENP8, PDCD7, PKM 
## PC_ 4 
## Positive:  USP8, GABPB1-AS1, TRPM7, GABPB1, SPPL2A, DTWD1, GLDN, GALK2, COPS2, SECISBP2L 
##     DMXL2, EID1, SHC4, SCG3, DUT, LYSMD2, MYEF2, TMOD2, SEMA6D, LEO1 
##     MAPK6, BLOC1S6, GNB5, GATM, MYO5A, SORD, B2M, SPG11, EIF3J, CTDSPL2 
## Negative:  NDN, SNRPN, MKRN3, SNURF, HERC2P7, UBE3A, HERC2P2, GABRB3, NIPA2, HERC2 
##     CYFIP1, TUBGCP5, HERC2P9, OR4M2, APBA2, TJP1, FAN1, MTMR10, SCG5, EMC7 
##     PGBD4, KATNBL1, EMC4, NOP10, GOLGA8A, GOLGA8B, AQR, ZNF770, C15orf41, MEIS2 
## PC_ 5 
## Positive:  MORF4L1, CTSH, TMED3, ST20, BCL2A1, ZFAND6, ARNT2, MESDC2, EFTUD1, RPS17 
##     UBE2Q2P3, RPS17L, CPEB1, WHAMM, FAM103A1, C15orf40, ULK3, CSK, BTBD1, EDC3 
##     TMOD2, LEO1, LYSMD2, MAPK6, TM6SF1, SCG3, GNB5, MYO5A, CLK3, DMXL2 
## Negative:  WASH3P, TARSL2, TM2D3, PCSK6, SNRPA1, VIMP, ASB7, LINS, MEF2A, LRRC28 
##     IGF1R, RGMA, CHD2, VPS33B, HDDC3, UNC45A, MAN2A2, CRTC3, NGRN, MAP2K1 
##     SNAPC5, TIPIN, RPL4, DIS3L, AAGAB, MEGF11, CIB1, RAB11A, C15orf61, DENND4A

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  ERVK13-1, PDPK1, ATP6V0C, AMDHD2, CEMP1, TBC1D24, KCTD5, SRRM2, ABCA3, TCEB2 
##     FLYWCH2, RNPS1, FLYWCH1, ECI1, PAQR4, E4F1, MLST8, HCFC1R1, TRAF7, THOC6 
##     PKD1, ZNF200, TSC2, NTHL1, TIGD7, TBL3, ZNF75A, SNHG9, MTRNR2L4, RPS2 
## Negative:  CHD9, RBL2, AKTIP, TOX3, FTO, SALL1, MMP2, CYLD, LPCAT2, NKD1 
##     GNAO1, BRD7, AMFR, ADCY7, CNEP1R1, ZNF423, SIAH1, LONP2, PHKB, ITFG1 
##     DNAJA2, PLLP, CX3CL1, GPT2, CIAPIN1, COQ9, C16orf87, POLR2C, ORC6, GPR56 
## PC_ 2 
## Positive:  FUS, KAT8, PYCARD, BCKDK, ITGAM, ITGAX, VKORC1, ARMC5, ZNF668, TGFB1I1 
##     STX4, C16orf58, STX1B, ZNF267, ORAI3, HERC2P4, RNF40, VPS35, PHKG2, SRCAP 
##     ORC6, PRR14, C16orf87, ZNF689, GPT2, ZNF785, DNAJA2, ZNF688, ZNF764, ITFG1 
## Negative:  TCEB2, SRRM2, KCTD5, ERVK13-1, FLYWCH2, PDPK1, CEMP1, FLYWCH1, AMDHD2, ATP6V0C 
##     CFDP1, PAQR4, BCAR1, ZFP1, TBC1D24, LDHD, GLG1, PSMD7, ABCA3, DHX38 
##     FA2H, WDR59, HCFC1R1, TMEM170A, RNPS1, TXNL4B, ECI1, THOC6, DHODH, E4F1 
## PC_ 3 
## Positive:  MGRN1, NUDT16L1, ANKS3, CDIP1, ZNF500, HMOX2, ROGDI, NMRAL1, DNAJA3, CORO7 
##     CREBBP, PAM16, GLYR1, TRAP1, CLUAP1, NAGPA, NAA60, ZNF597, ALG1, ZNF174 
##     FAM86A, MTRNR2L4, METTL22, ZNF75A, ABAT, TIGD7, TMEM186, ZNF200, PMM2, THOC6 
## Negative:  FA2H, GLG1, PSMD7, WDR59, DHX38, LDHD, ZFP1, TXNL4B, DHODH, BCAR1 
##     ZNF821, CFDP1, IST1, AP1G1, TMEM170A, ZNF19, TMEM231, ZNF23, GABARAPL2, HYDIN 
##     VAC14, ADAT1, MTSS1L, KARS, SF3B3, TERF2IP, COG4, DDX19A, MON1B, DDX19B 
## PC_ 4 
## Positive:  PRKCB, TNRC6A, RBBP6, DCTN5, SLC5A11, PALB2, ARHGAP17, NDUFAB1, LCMT1, UBFD1 
##     EARS2, NSMCE1, GGA2, GTF3C1, COG7, XPO6, SMG1P1, POLR3E, CLN3, EEF2K 
##     CCDC101, UQCRC2, EIF3C, RRN3P1, ATXN2L, IGSF6, TUFM, NFATC2IP, METTL9, SPNS1 
## Negative:  AMFR, GNAO1, LPCAT2, MMP2, FTO, AKTIP, RBL2, CHD9, PLLP, CX3CL1 
##     TOX3, CIAPIN1, COQ9, SALL1, POLR2C, GPR56, CYLD, KATNB1, NKD1, KIFC3 
##     USB1, BRD7, C16orf80, ADCY7, CCDC113, NDRG4, CNEP1R1, SETD6, ZNF423, CNOT1 
## PC_ 5 
## Positive:  RPUSD1, NARFL, CHTF18, HAGHL, LMF1, FAM173A, SOX8, UBE2I, BAIAP3, GNPTG 
##     UNKL, C16orf91, CLCN7, TELO2, CRAMP1L, MAPK8IP3, NME3, MRPS34, SPSB3, NUBP2 
##     HAGH, FAHD1, MSRB1, NDUFB10, RPS2, SNHG9, TBL3, NTHL1, TSC2, PKD1 
## Negative:  NUBP1, C16orf72, CLEC16A, USP7, LITAF, CARHSP1, PMM2, TMEM186, ABAT, METTL22 
##     FAM86A, ALG1, NAGPA, GLYR1, ROGDI, ZNF500, ANKS3, NUDT16L1, MGRN1, CDIP1 
##     HMOX2, NMRAL1, DNAJA3, CORO7, PAM16, CREBBP, TRAP1, CLUAP1, NAA60, ZNF597

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  LRRC37B, RHOT1, SUZ12, C17orf75, ZNF207, PSMD11, UTP6, TMEM98, CCL2, COPRS 
##     ZNF830, EVI2A, LIG3, RFFL, EVI2B, RAD51D, NLE1, OMG, AP2B1, CCL5 
##     NF1, CCL3, CCL4, ADAP2, CCL3L3, TEFM, CCL4L1, CRLF3, CCL3L1, LRRC37BP1 
## Negative:  MRPL27, XYLT2, LRRC59, RSAD1, PDK2, SPATA20, ANKRD40, KAT7, LUC7L3, SLC35B1 
##     TOB1, SPAG9, NME1, SPOP, NME2, PHB, UTP18, ZNF652, SNF8, CA10 
##     UBE2Z, COX11, ATP5G1, ATP1B2, SAT2, TP53, SOX15, CALCOCO2, WRAP53, MMD 
## PC_ 2 
## Positive:  TACO1, DCAF7, TANC2, STRADA, METTL2A, MED13, CCDC47, INTS2, DDX42, FTSJ3 
##     BCAS3, PSMC5, PPM1D, TEX2, APPBP2, POLG2, USP32, DDX5, HEATR6, MIR3064 
##     RNFT1, MIR5047, RPS6KB1, CEP95, TUBD1, SMURF2, VMP1, PTRH2, PLEKHM1P, CLTC 
## Negative:  PFN1, RNF167, SPAG7, CAMTA2, SLC25A11, ZFP3, PLD2, PSMB6, ZNF232, CXCL16 
##     ZNF594, MED11, ARRB2, PELP1, RABEP1, MYBBP1A, NUP88, UBE2G1, ANKFY1, RPAIN 
##     CYB5D2, ZZEF1, C1QBP, C17orf85, DERL2, ITGAE, MIS12, WSCD1, EMC6, TXNDC17 
## PC_ 3 
## Positive:  CA10, UTP18, COX11, MMD, NME2, TMEM100, PCTP, NME1, TRIM25, SPAG9 
##     COIL, SCPEP1, TOB1, AKAP1, MSI2, LUC7L3, ANKRD40, MRPS23, MRPL27, SPATA20 
##     RSAD1, LRRC59, XYLT2, KAT7, PDK2, SLC35B1, SPOP, VEZF1, PHB, ZNF652 
## Negative:  TP53I13, TAOK1, NUFIP2, GIT1, CORO6, TIAF1, ADAP2, TEFM, SSH2, CRLF3 
##     NF1, LRRC37BP1, NSRP1, GOSR1, BLMH, OMG, MYO18A, EVI2B, EVI2A, SEZ6 
##     COPRS, UTP6, PHF12, SUZ12, LRRC37B, FLOT2, RHOT1, C17orf75, ERAL1, ZNF207 
## PC_ 4 
## Positive:  ZNHIT3, MYO19, CCL4L2, CCL3L1, PIGW, CCL4L1, GGNBP2, CCL3L3, AATF, CCL4 
##     ACACA, TADA2A, PRKAR1A, ABCA8, CCL3, KCNJ16, SOX9, AMZ2, SLC39A11, DUSP14 
##     SSTR2, LINC00674, CCL5, COG1, SYNRG, FAM104A, AP2B1, KPNA2, NLE1, C17orf80 
## Negative:  TOM1L2, SREBF1, ATPAF2, SMCR5, RAI1, DRG2, PEMT, ALKBH5, RASD1, LLGL1 
##     MED9, COPS3, FLII, FLCN, MPRIP, TOP3A, USP32P1, SMCR8, CCDC144A, SHMT1 
##     ZNF624, CCDC144B, ZNF287, TVP23B, C17orf76-AS1, PRPSAP2, UBB, EPN2, PIGL, EPN2-AS1 
## PC_ 5 
## Positive:  NPEPPS, KPNB1, CDC27, OSBPL7, GOSR2, MRPL10, NSF, SCRN2, PNPO, CDK5RAP3 
##     ARL17A, NFE2L1, CBX1, LRRC37A2, SNX11, NSFP1, CALCOCO2, ATP5G1, ARL17B, UBE2Z 
##     SNF8, KANSL1-AS1, ZNF652, KANSL1, MAPT, PHB, LRRC37A4P, SPOP, PLEKHM1, SLC35B1 
## Negative:  C17orf80, FAM104A, CDC42EP4, RPL38, COG1, TTYH2, SSTR2, BTBD17, CD300A, SLC9A3R1 
##     SLC39A11, NAT9, SOX9, TMEM104, FDXR, KCNJ16, ABCA8, HID1, PRKAR1A, CDR2L 
##     AMZ2, ICT1, LINC00674, ATP5H, KPNA2, ARMC7, C17orf58, NT5C, BPTF, HN1

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  RPL17, RPL17-C18orf32, ACAA2, C18orf32, MBD1, DYM, CXXC1, CTIF, ME2, SMAD2 
##     ELAC1, SMAD4, IER3IP1, DCC, HDHD2, POLI, PIAS2, C18orf54, C18orf25, TCF4 
##     HAUS1, TXNL1, ATP5A1, WDR7, EPG5, SETBP1, ST8SIA3, PIK3C3, CELF4, FECH 
## Negative:  RIOK3, C18orf8, NPC1, TTC39C, CABYR, OSBPL1A, IMPACT, RBFA, TXNL4A, ATP9B 
##     ZNF521, MBP, TSHZ1, SS18, CNDP1, CNDP2, CHST9, FAM69C, CDH2, CYB5A 
##     TIMM21, TRAPPC8, SOCS6, RTTN, RNF138, TMX3, DSEL, DTNA, SERPINB8, MAPRE2 
## PC_ 2 
## Positive:  RBFA, TXNL4A, ATP9B, MBP, TSHZ1, CNDP1, CNDP2, FAM69C, CYB5A, TIMM21 
##     SOCS6, RTTN, TMX3, DSEL, SERPINB8, VPS4B, KDSR, PHLPP1, KIAA1468, PIGN 
##     CDH20, LMAN1, SEC11C, ZNF532, NARS, FECH, ST8SIA3, WDR7, TXNL1, TCF4 
## Negative:  IMPACT, ZNF521, OSBPL1A, SS18, CABYR, CHST9, TTC39C, CDH2, NPC1, TRAPPC8 
##     C18orf8, RNF138, RIOK3, DTNA, MAPRE2, ZNF397, ZSCAN30, ZNF271, ZNF24, INO80C 
##     GALNT1, C18orf21, RPRD1A, SLC39A6, ELP2, TPGS2, KIAA1328, CELF4, PIK3C3, SETBP1 
## PC_ 3 
## Positive:  RIOK3, C18orf8, NPC1, TTC39C, CABYR, OSBPL1A, IMPACT, ZNF521, RBFA, SS18 
##     TXNL4A, ATP9B, MBP, TSHZ1, CNDP1, CHST9, CNDP2, FAM69C, CDH2, CYB5A 
##     TIMM21, SOCS6, TRAPPC8, RTTN, TMX3, DSEL, RNF138, SERPINB8, VPS4B, DTNA 
## Negative:  DYM, C18orf32, CTIF, SMAD2, RPL17-C18orf32, RPL17, IER3IP1, ACAA2, HDHD2, MBD1 
##     PIAS2, CXXC1, C18orf25, ME2, HAUS1, ELAC1, ATP5A1, SMAD4, EPG5, DCC 
##     SETBP1, POLI, PIK3C3, C18orf54, CELF4, TCF4, KIAA1328, TXNL1, TPGS2, WDR7 
## PC_ 4 
## Positive:  RBFA, TXNL4A, ATP9B, MBP, TSHZ1, CNDP1, CNDP2, FAM69C, CYB5A, TPGS2 
##     ELP2, KIAA1328, CELF4, SLC39A6, PIK3C3, RPRD1A, TIMM21, SETBP1, C18orf21, EPG5 
##     GALNT1, ATP5A1, SOCS6, HAUS1, INO80C, C18orf25, RTTN, ZNF24, PIAS2, HDHD2 
## Negative:  FECH, ST8SIA3, NARS, WDR7, ZNF532, TXNL1, TCF4, SEC11C, C18orf54, RIOK3 
##     C18orf8, LMAN1, POLI, NPC1, TTC39C, DCC, CABYR, CDH20, SMAD4, OSBPL1A 
##     IMPACT, ELAC1, PIGN, ZNF521, ME2, KIAA1468, SS18, CXXC1, CHST9, MBD1 
## PC_ 5 
## Positive:  RIOK3, C18orf8, NPC1, C18orf32, RPL17-C18orf32, DYM, RPL17, CTIF, ACAA2, TTC39C 
##     SMAD2, MBD1, CXXC1, IER3IP1, CABYR, RBFA, ME2, HDHD2, TXNL4A, ELAC1 
##     ATP9B, PIAS2, OSBPL1A, MBP, SMAD4, TSHZ1, C18orf25, CNDP1, DCC, IMPACT 
## Negative:  PIGN, CDH20, KIAA1468, ZNF271, LMAN1, ZNF24, ZSCAN30, SEC11C, PHLPP1, INO80C 
##     ZNF397, GALNT1, MAPRE2, ZNF532, KDSR, C18orf21, DTNA, RPRD1A, NARS, VPS4B 
##     SLC39A6, RNF138, ELP2, SERPINB8, FECH, TPGS2, TRAPPC8, DSEL, KIAA1328, ST8SIA3

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  POLD1, NAPSB, JOSD2, NR1H2, ASPDH, C19orf48, VRK3, KLK6, TBC1D17, NUP62 
##     PNKP, PTOV1, ETFB, FUZ, SIGLEC10, AP2A1, SIGLEC8, CPT1C, FPR1, PRMT1 
##     IRF3, ZNF577, NOSIP, ZNF649, FCGRT, ZNF350, RPS11, ZNF614, RPL13A, PPP2R1A 
## Negative:  ZNF506, ZNF253, ZNF14, ATP13A1, ZNF93, LPAR2, ZNF682, YJEFN3, ZNF737, NDUFA13 
##     MAU2, ZNF626, SUGP1, NCAN, ZNF85, NR2C2AP, ZNF430, RFXANK, ZNF714, MEF2BNB 
##     ZNF431, TMEM161A, ZNF708, SLC25A42, ZNF738, ARMC6, ZNF493, SUGP2, ZNF429, HOMER3 
## PC_ 2 
## Positive:  ZNF586, ZNF134, ZNF211, ZNF550, ZNF773, ZNF772, ZNF17, ZNF548, TRAPPC2P1, ZNF460 
##     ZNF805, ZNF71, ZFP28, ZNF471, ZNF667, ZNF583, ERCC1, BLOC1S3, TRAPPC6A, FOSB 
##     GEMIN7, EML2, PNMAL1, PPP5C, HIF3A, CALM3, QPCTL, DMPK, SYMPK, ZNF542 
## Negative:  NCAN, NR2C2AP, SUGP1, RFXANK, MAU2, MEF2BNB, NDUFA13, TMEM161A, YJEFN3, SLC25A42 
##     LPAR2, ARMC6, ATP13A1, SUGP2, ZNF14, HOMER3, ZNF506, DDX49, ZNF253, COPE 
##     ZNF93, CRTC1, ZNF682, TMEM59L, ZNF737, C19orf60, ZNF626, ZNF85, UBA52, ZNF430 
## PC_ 3 
## Positive:  RPSAP58, ZNF675, ZNF91, ZNF724P, ZNF676, ZNF43, ZNF181, ZNF100, GRAMD1A, ZNF429 
##     FXYD7, ZNF493, FXYD5, USF2, ZNF738, MAG, ZNF708, TMEM147, ZNF431, RBM42 
##     COX6B1, ZNF714, IGFLR1, ZNF430, U2AF1L4, ZNF85, PSENEN, ARHGAP33, ZNF626, APLP1 
## Negative:  UBL5, PIN1, FBXL12, ZNF812, OLFM2, ZNF562, ZNF561, C19orf66, ZNF121, PPAN 
##     ZNF426, EIF3G, ZNF266, ZNF177, DNMT1, S1PR2, MRPL4, ICAM1, FDX1L, RAVER1 
##     TYK2, CDC37, KEAP1, LSM7, GADD45B, LMNB2, SPPL2B, GNG7, OAZ1, TIMM13 
## PC_ 4 
## Positive:  AP3D1, MOB3A, PLEKHJ1, BTBD2, SCAMP4, SF3A2, UQCR11, OAZ1, MBD3, LSM7 
##     C19orf25, SPPL2B, TIMM13, APC2, LMNB2, GADD45B, GNG7, SLC39A3, SGTA, ZNF580 
##     ZNF581, ZNF542, ISOC2, ZNF583, SHISA7, RPL28, ZNF667, HSPBP1, ZNF471, ZFP28 
## Negative:  MRPL4, S1PR2, ICAM1, DNMT1, EIF3G, FDX1L, PPAN, RAVER1, C19orf66, TYK2 
##     OLFM2, CDC37, PIN1, KEAP1, UBL5, FBXL12, ZNF812, ZNF562, ZNF561, ZNF121 
##     ZNF426, ZNF266, ZNF177, NFKBID, HCST, TYROBP, APLP1, SDHAF1, ARHGAP33, ALKBH6 
## PC_ 5 
## Positive:  ZNF773, ZNF772, ZNF17, ZNF550, ZNF548, ZNF134, TRAPPC2P1, ZNF211, ZNF460, ZNF586 
##     ZNF805, ZNF71, ZFP28, ZNF471, ZNF667, TYK2, RAVER1, CDC37, KEAP1, ZNF583 
##     FDX1L, ZNF542, ICAM1, ZNF581, MRPL4, S1PR2, ZNF580, DNMT1, ISOC2, EIF3G 
## Negative:  GEMIN7, TRAPPC6A, BLOC1S3, CLPTM1, ERCC1, SNRPD2, EML2, FOSB, APOC2, APOC1 
##     QPCTL, APOE, DMPK, TOMM40, SYMPK, PVR, HIF3A, ZNF227, ZNF226, PPP5C 
##     ZNF234, PNMAL1, ZNF225, ZNF221, ZNF404, CALM3, LYPD5, SMG9, PLAUR, ZNF428

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  SRSF6, L3MBTL1, CHD6, IFT52, TTPAL, ZHX3, SERINC3, PLCG1, PKIG, TOP1 
##     ADA, MAFB, DHX35, YWHAB, ACTR5, TOMM34, SNHG11, STK4, KIAA1755, SYS1 
##     RPRD1B, DBNDD2, TTI1, PIGT, CTNNBL1, DNTTIP1, BLCAP, SNX21, SRC, ACOT8 
## Negative:  NPEPL1, STX16, VAPB, MTRNR2L3, RAE1, C20orf112, BMP7, COMMD7, MAPRE1, RTFDC1 
##     CDK5RAP1, CSTF1, CBFA2T2, DOK5, NECAB3, PFDN4, PXMP4, BCAS1, RALY, ZFP64 
##     EIF2S2, ATP9A, AHCY, MOCS3, ITCH, DPM1, DYNLRB1, ADNP, MAP1LC3A, PTPN1 
## PC_ 2 
## Positive:  EDEM2, EIF6, TRPC4AP, GSS, CEP250, ACSS2, ERGIC3, GGT7, TP53INP2, CPNE1 
##     NCOA6, RBM12, PIGU, NFS1, MAP1LC3A, ROMO1, DYNLRB1, RBM39, ITCH, PHF20 
##     AHCY, SCAND1, EIF2S2, RALY, LINC00657, PXMP4, EPB41L1, NECAB3, AAR2, CBFA2T2 
## Negative:  SLC9A8, RNF114, ZFAS1, ZNFX1, UBE2V1, DDX27, TMEM189, STAU1, PTPN1, CSE1L 
##     ADNP, DPM1, ARFGEF2, MOCS3, PREX1, ATP9A, ZFP64, SULF2, BCAS1, NCOA3 
##     PFDN4, ZMYND8, DOK5, TP53RK, CSTF1, ZNF334, RTFDC1, BMP7, ELMO2, RAE1 
## PC_ 3 
## Positive:  L3MBTL1, IFT52, SRSF6, TTPAL, CHD6, SERINC3, ZHX3, PKIG, PLCG1, ADA 
##     TOP1, YWHAB, MAFB, TOMM34, STK4, DHX35, SYS1, ACTR5, DBNDD2, SNHG11 
##     PIGT, KIAA1755, DNTTIP1, RPRD1B, SNX21, TTI1, ACOT8, CTNNBL1, ZSWIM1, BLCAP 
## Negative:  NPEPL1, STX16, VAPB, MTRNR2L3, RAE1, C20orf112, BMP7, COMMD7, MAPRE1, RTFDC1 
##     CDK5RAP1, CSTF1, CBFA2T2, DOK5, NECAB3, PFDN4, PXMP4, RALY, BCAS1, EIF2S2 
##     ZFP64, AHCY, ATP9A, ITCH, MOCS3, DYNLRB1, DPM1, MAP1LC3A, ADNP, PIGU 
## PC_ 4 
## Positive:  NPEPL1, STX16, VAPB, MTRNR2L3, RAE1, BMP7, RTFDC1, CSTF1, DOK5, PFDN4 
##     RPN2, RBL1, MANBAL, SAMHD1, SOGA1, SRC, NDRG3, BLCAP, C20orf24, CTNNBL1 
##     BCAS1, DLGAP4, TTI1, AAR2, RPRD1B, ZFP64, EPB41L1, KIAA1755, LINC00657, SNHG11 
## Negative:  C20orf112, COMMD7, MAPRE1, CDK5RAP1, CBFA2T2, NECAB3, PXMP4, RALY, EIF2S2, AHCY 
##     ITCH, CD40, NCOA5, ZNF335, SLC35C2, PCIF1, PLTP, ELMO2, CTSA, NEURL2 
##     ZNF334, DYNLRB1, ZSWIM1, TP53RK, ACOT8, ZMYND8, SNX21, NCOA3, DNTTIP1, MAP1LC3A 
## PC_ 5 
## Positive:  C20orf112, COMMD7, MAPRE1, NPEPL1, STX16, CDK5RAP1, VAPB, MTRNR2L3, CBFA2T2, RAE1 
##     BMP7, NECAB3, RTFDC1, PXMP4, CSTF1, RALY, TTPAL, IFT52, SERINC3, L3MBTL1 
##     PKIG, SRSF6, ADA, CHD6, DOK5, YWHAB, ZHX3, TOMM34, STK4, PLCG1 
## Negative:  DDX27, ZNFX1, STAU1, ZFAS1, CSE1L, SLC9A8, ARFGEF2, RNF114, RBM12, CPNE1 
##     NFS1, PREX1, ERGIC3, ROMO1, CEP250, RBM39, UBE2V1, EIF6, SULF2, PHF20 
##     EDEM2, NCOA3, TRPC4AP, SCAND1, TMEM189, LINC00657, GSS, ZMYND8, PTPN1, EPB41L1

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## Warning: Requested number is larger than the number of available items (38).
## Setting to 38.

## Warning: Requested number is larger than the number of available items (38).
## Setting to 38.

## Warning: Requested number is larger than the number of available items (38).
## Setting to 38.

## Warning: Requested number is larger than the number of available items (38).
## Setting to 38.

## Warning: Requested number is larger than the number of available items (38).
## Setting to 38.

## PC_ 1 
## Positive:  CCT8, USP16, BACH1, RWDD2B, TIAM1, LTN1, SOD1, N6AMT1, SCAF4, ADAMTS1 
##     MIS18A, APP, URB1, GABPA, C21orf119, ATP5J, C21orf59, JAM2, SYNJ1 
## Negative:  IFNGR2, IFNAR1, TEKT4P2, IL10RB, HSPA13, IFNAR2, SAMSN1, LINC00478, OLIG1, C21orf37 
##     OLIG2, CXADR, BTG3, C21orf62, LINC00320, PAXBP1, NCAM2, PAXBP1-AS1, MRPL39 
## PC_ 2 
## Positive:  IFNGR2, IFNAR1, IL10RB, IFNAR2, OLIG1, OLIG2, C21orf62, PAXBP1, PAXBP1-AS1, SYNJ1 
##     C21orf59, C21orf119, URB1, MIS18A, SCAF4, SOD1, TIAM1, BACH1, CCT8 
## Negative:  TEKT4P2, HSPA13, SAMSN1, LINC00478, C21orf37, CXADR, BTG3, LINC00320, NCAM2, MRPL39 
##     JAM2, ATP5J, GABPA, APP, ADAMTS1, N6AMT1, LTN1, RWDD2B, USP16 
## PC_ 3 
## Positive:  USP16, CCT8, RWDD2B, BACH1, LTN1, TIAM1, SOD1, N6AMT1, SCAF4, ADAMTS1 
##     MIS18A, APP, URB1, GABPA, C21orf119, ATP5J, C21orf59, JAM2, MRPL39 
## Negative:  TEKT4P2, IFNGR2, HSPA13, IFNAR1, SAMSN1, IL10RB, LINC00478, IFNAR2, C21orf37, OLIG1 
##     CXADR, OLIG2, BTG3, C21orf62, LINC00320, PAXBP1, NCAM2, PAXBP1-AS1, SYNJ1 
## PC_ 4 
## Positive:  IFNGR2, GABPA, ATP5J, APP, IFNAR1, JAM2, ADAMTS1, N6AMT1, MRPL39, IL10RB 
##     NCAM2, LTN1, IFNAR2, LINC00320, RWDD2B, OLIG1, BTG3, USP16, OLIG2 
## Negative:  TEKT4P2, URB1, C21orf119, MIS18A, HSPA13, SCAF4, C21orf59, SOD1, SAMSN1, SYNJ1 
##     TIAM1, PAXBP1-AS1, LINC00478, BACH1, PAXBP1, C21orf37, CCT8, C21orf62, CXADR 
## PC_ 5 
## Positive:  MRPL39, NCAM2, SYNJ1, C21orf59, JAM2, PAXBP1-AS1, LINC00320, PAXBP1, C21orf119, ATP5J 
##     C21orf62, BTG3, URB1, GABPA, OLIG2, CXADR, MIS18A, APP, OLIG1 
## Negative:  USP16, IFNGR2, CCT8, RWDD2B, TEKT4P2, BACH1, HSPA13, IFNAR1, LTN1, TIAM1 
##     SAMSN1, IL10RB, N6AMT1, SOD1, LINC00478, IFNAR2, ADAMTS1, SCAF4, C21orf37

## Computing nearest neighbor graph

## Computing SNN

## Centering and scaling data matrix

## PC_ 1 
## Positive:  RABL2B, CHKB, CPT1B, SCO2, NCAPH2, LMF2, PPP6R2, DENND6B, PLXNB2, MAPK12 
##     TUBGCP6, TRABD, GSTT2B, MLC1, DDT, CRELD2, GSTT2, ALG12, GSTT1, FAM19A5 
##     CABIN1, TBC1D22A, SPECC1L, GUCD1, SNRPD3, FAM211B, SGSM1, CRYBB2P1, TTLL12, SEZ6L 
## Negative:  CYTH4, MFNG, MPST, CDC42EP1, TST, GGA1, NCF4, PDXP, IFT27, LGALS1 
##     EIF3D, FOXRED2, TXN2, MYH9, APOL2, H1F0, GCAT, APOL4, ANKRD54, RBFOX2 
##     EIF3L, MCM5, POLR2F, HMOX1, PLA2G6, TOM1, MAFF, HMGXB4, TMEM184B, CSNK1E 
## PC_ 2 
## Positive:  ZMAT5, NF2, UQCR10, NIPSNAP1, THOC5, ASCC2, AP1B1, MTMR3, RASL10A, OSM 
##     EWSR1, GATSL3, TBC1D10A, RHBDD3, SF3A1, ZNRF3-AS1, SEC14L2, MTFP1, XBP1, GAL3ST1 
##     PES1, CCDC117, OSBP2, MORC2-AS1, HSCB, TUG1, TTC28, SELM, TTC28-AS1, RNF185 
## Negative:  PMM1, POLR3H, ACO2, PHF5A, DESI1, TOB2, XRCC6, TEF, NHP2L1, SREBF2 
##     ZC3H7B, NAGA, RANGAP1, NDUFA6, CHADL, L3MBTL2, RRP7A, EP300, RRP7B, RBX1 
##     POLDIP3, XPNPEP3, CYB5R3, ST13, ARFGAP3, SLC25A17, PACSIN2, MKL1, TTLL1, SGSM3 
## PC_ 3 
## Positive:  LGALS1, PDXP, GGA1, CDC42EP1, H1F0, MFNG, CYTH4, GCAT, MPST, ANKRD54 
##     EIF3L, TST, POLR2F, NCF4, PLA2G6, IFT27, MAFF, TMEM184B, EIF3D, CSNK1E 
##     FOXRED2, DDX17, TXN2, CBY1, MYH9, TOMM22, APOL2, JOSD1, APOL4, GTPBP1 
## Negative:  PLXNB2, MAPK12, DENND6B, TUBGCP6, PPP6R2, TRABD, LMF2, NCAPH2, MLC1, SCO2 
##     CRELD2, CPT1B, CHKB, ALG12, RABL2B, FAM19A5, TBC1D22A, TTLL12, TSPO, MCAT 
##     TTLL1, PACSIN2, FAM211B, SGSM1, SNRPD3, CRYBB2P1, GUCD1, SPECC1L, ARFGAP3, SEZ6L 
## PC_ 4 
## Positive:  GSTT2B, DDT, GSTT2, GSTT1, CABIN1, SPECC1L, GUCD1, SNRPD3, FAM211B, SGSM1 
##     CRYBB2P1, SEZ6L, HPS4, TFIP11, MIAT, PITPNB, TTC28-AS1, TTC28, HSCB, CCDC117 
##     ADSL, SGSM3, TNRC6B, MKL1, RPS19BP1, ATF4, SLC25A17, TAB1, ST13, SYNGR1 
## Negative:  RABL2B, CHKB, CPT1B, SCO2, NCAPH2, LMF2, PPP6R2, DENND6B, PLXNB2, MAPK12 
##     TUBGCP6, TRABD, MLC1, CRELD2, ALG12, FAM19A5, TBC1D22A, SYN3, FBXO7, TIMP3 
##     YWHAH, HMGXB4, TOM1, DEPDC5, HMOX1, PRR14L, MCM5, PISD, RBFOX2, EIF4ENIF1 
## PC_ 5 
## Positive:  ACO2, POLR3H, PHF5A, PMM1, TOB2, DESI1, TEF, XRCC6, PES1, ZC3H7B 
##     GAL3ST1, OSBP2, MORC2-AS1, NHP2L1, MTFP1, RANGAP1, TUG1, SEC14L2, SREBF2, SF3A1 
##     SELM, CHADL, TBC1D10A, NAGA, RNF185, GATSL3, NDUFA6, L3MBTL2, OSM, PIK3IP1 
## Negative:  GSTT2B, RABL2B, DDT, CHKB, GSTT2, CPT1B, GSTT1, SCO2, NCAPH2, CABIN1 
##     LMF2, SPECC1L, PPP6R2, DENND6B, GUCD1, PLXNB2, LGALS1, PDXP, H1F0, GGA1 
##     MAPK12, GCAT, ANKRD54, SNRPD3, CDC42EP1, EIF3L, MFNG, POLR2F, TUBGCP6, CYTH4

## Computing nearest neighbor graph

## Computing SNN

Basic ouput from running inferCNV.

3 Additional Information

3.1 Online Documentation

For additional explanations on files, usage, and a tutorial please visit the wiki.

3.2 TrinityCTAT

This tool is a part of the TrinityCTAT toolkit focused on leveraging the use of RNA-Seq to better understand cancer transcriptomes. To find out more please visit TrinityCTAT

3.3 Applications

This methodology was used in:

Anoop P. Patel et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014 Jun 20: 1396-1401

Tirosh I et al.Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq. Science. 2016 Apr 8;352(6282):189-96

4 Session info

## R Under development (unstable) (2022-10-25 r83175)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.1 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.17-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_GB              LC_COLLATE=C              
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] infercnv_1.15.0  BiocStyle_2.27.0
## 
## loaded via a namespace (and not attached):
##   [1] RcppAnnoy_0.0.20            splines_4.3.0              
##   [3] later_1.3.0                 bitops_1.0-7               
##   [5] tibble_3.1.8                polyclip_1.10-4            
##   [7] rpart_4.1.19                lifecycle_1.0.3            
##   [9] fastcluster_1.2.3           edgeR_3.41.0               
##  [11] doParallel_1.0.17           globals_0.16.1             
##  [13] lattice_0.20-45             MASS_7.3-58.1              
##  [15] magrittr_2.0.3              limma_3.55.0               
##  [17] plotly_4.10.0               sass_0.4.2                 
##  [19] rmarkdown_2.17              jquerylib_0.1.4            
##  [21] yaml_2.3.6                  httpuv_1.6.6               
##  [23] Seurat_4.2.0                sctransform_0.3.5          
##  [25] spatstat.core_2.4-4         sp_1.5-0                   
##  [27] spatstat.sparse_3.0-0       reticulate_1.26            
##  [29] rgeos_0.5-9                 cowplot_1.1.1              
##  [31] pbapply_1.5-0               DBI_1.1.3                  
##  [33] RColorBrewer_1.1-3          multcomp_1.4-20            
##  [35] abind_1.4-5                 zlibbioc_1.45.0            
##  [37] Rtsne_0.16                  GenomicRanges_1.51.0       
##  [39] purrr_0.3.5                 BiocGenerics_0.45.0        
##  [41] RCurl_1.98-1.9              TH.data_1.1-1              
##  [43] sandwich_3.0-2              GenomeInfoDbData_1.2.9     
##  [45] IRanges_2.33.0              S4Vectors_0.37.0           
##  [47] ggrepel_0.9.1               irlba_2.3.5.1              
##  [49] listenv_0.8.0               spatstat.utils_3.0-1       
##  [51] goftest_1.2-3               spatstat.random_3.0-0      
##  [53] fitdistrplus_1.1-8          parallelly_1.32.1          
##  [55] leiden_0.4.3                codetools_0.2-18           
##  [57] coin_1.4-2                  DelayedArray_0.25.0        
##  [59] tidyselect_1.2.0            futile.logger_1.4.3        
##  [61] rjags_4-13                  matrixStats_0.62.0         
##  [63] stats4_4.3.0                jsonlite_1.8.3             
##  [65] ellipsis_0.3.2              progressr_0.11.0           
##  [67] ggridges_0.5.4              survival_3.4-0             
##  [69] iterators_1.0.14            foreach_1.5.2              
##  [71] tools_4.3.0                 ica_1.0-3                  
##  [73] Rcpp_1.0.9                  glue_1.6.2                 
##  [75] gridExtra_2.3               xfun_0.34                  
##  [77] mgcv_1.8-41                 MatrixGenerics_1.11.0      
##  [79] GenomeInfoDb_1.35.0         dplyr_1.0.10               
##  [81] formatR_1.12                BiocManager_1.30.19        
##  [83] fastmap_1.1.0               fansi_1.0.3                
##  [85] caTools_1.18.2              digest_0.6.30              
##  [87] parallelDist_0.2.6          R6_2.5.1                   
##  [89] mime_0.12                   colorspace_2.0-3           
##  [91] scattermore_0.8             gtools_3.9.3               
##  [93] tensor_1.5                  spatstat.data_3.0-0        
##  [95] utf8_1.2.2                  tidyr_1.2.1                
##  [97] generics_0.1.3              data.table_1.14.4          
##  [99] httr_1.4.4                  htmlwidgets_1.5.4          
## [101] uwot_0.1.14                 pkgconfig_2.0.3            
## [103] gtable_0.3.1                modeltools_0.2-23          
## [105] lmtest_0.9-40               SingleCellExperiment_1.21.0
## [107] XVector_0.39.0              htmltools_0.5.3            
## [109] bookdown_0.29               SeuratObject_4.1.2         
## [111] scales_1.2.1                Biobase_2.59.0             
## [113] png_0.1-7                   phyclust_0.1-32            
## [115] knitr_1.40                  lambda.r_1.2.4             
## [117] reshape2_1.4.4              coda_0.19-4                
## [119] nlme_3.1-160                cachem_1.0.6               
## [121] zoo_1.8-11                  stringr_1.4.1              
## [123] KernSmooth_2.23-20          parallel_4.3.0             
## [125] miniUI_0.1.1.1              libcoin_1.0-9              
## [127] pillar_1.8.1                grid_4.3.0                 
## [129] vctrs_0.5.0                 gplots_3.1.3               
## [131] RANN_2.6.1                  promises_1.2.0.1           
## [133] xtable_1.8-4                cluster_2.1.4              
## [135] evaluate_0.17               locfit_1.5-9.6             
## [137] mvtnorm_1.1-3               cli_3.4.1                  
## [139] compiler_4.3.0              futile.options_1.0.1       
## [141] rlang_1.0.6                 future.apply_1.9.1         
## [143] argparse_2.1.6              plyr_1.8.7                 
## [145] stringi_1.7.8               viridisLite_0.4.1          
## [147] deldir_1.0-6                assertthat_0.2.1           
## [149] munsell_0.5.0               lazyeval_0.2.2             
## [151] spatstat.geom_3.0-3         Matrix_1.5-1               
## [153] patchwork_1.1.2             future_1.28.0              
## [155] ggplot2_3.3.6               shiny_1.7.3                
## [157] highr_0.9                   SummarizedExperiment_1.29.0
## [159] ROCR_1.0-11                 igraph_1.3.5               
## [161] RcppParallel_5.1.5          bslib_0.4.0                
## [163] ape_5.6-2