diff --git a/intro-pathway-analysis-visualization/Hands-on.pdf b/intro-pathway-analysis-visualization/Hands-on.pdf deleted file mode 100644 index 645b5d5..0000000 Binary files a/intro-pathway-analysis-visualization/Hands-on.pdf and /dev/null differ diff --git a/intro-pathway-analysis-visualization/Hands-on_PathwayAnalysis.docx b/intro-pathway-analysis-visualization/Hands-on_PathwayAnalysis.docx index 1a86bf0..b6f72d6 100644 Binary files a/intro-pathway-analysis-visualization/Hands-on_PathwayAnalysis.docx and b/intro-pathway-analysis-visualization/Hands-on_PathwayAnalysis.docx differ diff --git a/intro-pathway-analysis-visualization/Hands-on_PathwayAnalysis.pdf b/intro-pathway-analysis-visualization/Hands-on_PathwayAnalysis.pdf index e55b4c4..a941079 100644 Binary files a/intro-pathway-analysis-visualization/Hands-on_PathwayAnalysis.pdf and b/intro-pathway-analysis-visualization/Hands-on_PathwayAnalysis.pdf differ diff --git a/intro-pathway-analysis-visualization/lung.expr.dn.txt b/intro-pathway-analysis-visualization/lung.expr.dn.txt index caeade9..7ab2ad9 100644 --- a/intro-pathway-analysis-visualization/lung.expr.dn.txt +++ b/intro-pathway-analysis-visualization/lung.expr.dn.txt @@ -1,641 +1,516 @@ -FGR -PDK4 -ST7 -SLC4A1 -ITGAL -CX3CL1 -CEACAM21 -SEMA3G -SLC6A13 -BTK -ABHD5 -ANOS1 -ALOX5 -CALCOCO1 -MAN2B2 -IL20RA -SLC11A1 -MARCO -FHL1 -EHD2 -HSD17B6 -PRKCH -ARHGAP31 -DAPK2 -MSR1 -ADRB1 -ARHGAP6 -CCDC85A -RASGRF1 -TBXAS1 -LIMCH1 -CHI3L2 -CALCRL -SPI1 -CLDN18 -KLF6 -PLPP1 -RASGRP2 -MAOB -TGFBR3 -PTPN21 -RPS6KA2 -LMCD1 -CYBRD1 -LIMS2 -FERMT2 -CD5L -FRY -MGLL -RBMS2 -APBB1IP -ITGA8 -EDN1 -ITM2A -TNS1 -SESN1 -CPB2 -COL4A4 -CACNA1S -LRP2 -PILRA -CASS4 -SIGLEC1 -TBX5 -NOS1 -NLRC4 -JPH4 -DPYSL2 -ADA2 -FMO2 -SH2D3C -SORBS1 -GADD45B -MFNG -PIK3IP1 -TTC28 -CBX7 -PDGFB -RIN3 -RASSF2 -ANGPT4 -CDS2 -SIRPB1 -CCM2L -SAMHD1 -RENBP -RS1 -VGLL1 -CAB39L -ACP5 -SGCG -RGCC -WFDC1 -FOXF1 -GGA2 -RASL12 -CA2 -CD37 -CLEC4M -PRX -DENND3 -SIGLEC5 -RASIP1 -CAV2 -CAV1 -HOXA5 -CPED1 -TSPAN13 -SLC1A1 -ENG -TYRP1 -PIP5K1B -PTGDS -PALD1 -VSIR -SPOCK2 -RGS9 -4-Sep -P2RX1 -SLC6A4 -SGCA -HLF -SLC16A6 -ODAM -WFS1 -SOD3 -CRYAB -GALNT18 -SLC15A3 -HPS5 -VWF -SELPLG -BIN2 -LIN7A -ACSS3 -TNS2 -CREBL2 -OAS2 -ART4 -C12orf49 -CHPT1 -LPCAT3 -SERINC1 -SASH1 -MDGA1 -BMP5 -FHL5 -KHDRBS2 -EPM2A -CCND3 -CLIC5 -NPR3 -HYAL1 -EFCC1 -PLSCR4 -ARHGEF26 -VIPR1 -TNNC1 -ACADL -EFEMP1 -HPCAL1 -PLCL1 -PCYOX1 -EPAS1 -C1orf21 -LEPR -PRG4 -NCF2 -ADGRL2 -STX12 -FILIP1 -CNR1 -PLAGL1 -TCF21 -KLF9 -C1orf198 -LTBP2 -FLVCR2 -LGALSL -IFIT3 -IFIT2 -DUSP1 -TEK -MOB3B -KCNJ5 -CHRNA2 -PDLIM2 -TBX2 -TBX4 -PLBD1 -CAT -FABP3 -CCRL2 -SASH3 -RAMP3 -GLIPR2 -RECK -HVCN1 -BHLHE41 -NECAB1 -NCKAP1L -C4BPA -FAM124B -PREX1 -MOCS1 -AHNAK -EFNB2 -TMEM255A -S1PR4 -RHOJ -ARMCX1 -FGD3 -MASP1 -F2RL3 -HIP1 -MGAT3 -CGNL1 -SLC44A2 -CDO1 -ARHGEF6 -STARD8 -USHBP1 -RGN -COX4I2 -HIGD1B -ADGRE3 -SH3BP5 -AOC3 -RAMP2 -TMEM204 -RAI2 -PPARG -CARD6 -HSPA12B -SSTR4 -MYH10 -KL -PRAM1 -PDZD2 -GIMAP6 -GIMAP4 -LYVE1 -HSD17B4 -CNTN6 -GSTM5 -SORT1 -CD101 -ADAMTS8 -FAM189A2 -TBX3 -OASL -CD36 -LMO2 -STX11 -CPM -SLC19A3 -CYP27A1 -THSD1 -LMO7 -EDNRB -TM6SF1 -TEX2 -SCN7A -GYPC -TMOD1 -TLR4 -RNF144B -ARRB1 -SLCO2B1 -LRRC32 -SDCBP -TRPC6 -FXYD6 -PAQR5 -SMAD6 -PLCB2 -SEMA6D -GCOM1 -DNASE2B -RBP4 -PLA2G12B -AOX1 -ARHGAP24 -PRKG2 -FGF2 -ANXA3 -SLC39A8 -PARVG -ERP27 -GABARAPL1 -FGD4 -ACVRL1 -JDP2 -FBLN5 -CYP1A2 -ITGAX -NKD1 -ABCA8 -GATA6 -SLC14A1 -PNMT -MYO1F -SLC47A1 -FCN3 -C1orf162 -RXRG -RGS5 -ADAMTSL4 -ZNF385B -CNTN4 -CSRNP1 -CTDSPL -STAC -ADPRH -AGTR1 -SLIT2 -NKD2 -HMGCLL1 -PRSS35 -TMEM140 -TMEM47 -AWAT2 -GPC3 -DOK2 -TACC1 -RSPO2 -PLIN2 -CDKN2B -STOM -ST8SIA6 -ANKRD1 -ESAM -SIDT2 -CLEC1A -GPM6A -HSPB8 -IGSF10 -SPARCL1 -BANK1 -UBASH3B -ROBO4 -ABI3BP -ANGPT1 -DISP1 -WNT3A -FGD5 -GRIA1 -VSIG4 -ELMO1 -AFF2 -GNAQ -ADAMTSL3 -TSPAN7 -TDRD9 -RAB11FIP1 -TSC22D3 -KCNJ15 -TMEM164 -SNX22 -MRAS -FAM46B -SHROOM4 -ITLN2 -SCUBE1 -ACE -LRRC36 -PTGIR -ABCG1 -JAML -IL6R -PTH1R -FGFR4 -SIGLEC16 -CD300LG -PLPP3 -NTNG1 -KCNT2 -C1orf115 -PKDCC -NOSTRIN -ARHGAP25 -EIF4E3 -TGFBR2 -PRICKLE2 -DNASE1L3 -CPA3 -CLEC3B -LRRC2 -KLF15 -EMCN -HHIP -ENPP6 -CITED2 -BMPER -KIAA1324L -FABP5 -SOX17 -SBSPON -GPR146 -CA3 -DCSTAMP -MAMDC2 -SVEP1 -FBP1 -VEGFD -OTUD1 -DEPP1 -C10orf25 -VSTM4 -JCAD -BTNL9 -CYYR1 -SYNPO2L -TMEM130 -MFAP4 -SCNN1G -MS4A7 -MS4A15 -TEF -DPEP2 -CA4 -GPD1 -KIR3DL1 -PPP1R14A -CD300C -FAM107A -CX3CR1 -CAVIN2 -AXIN2 -IL7R -WFDC12 -NPNT -ATOH8 -PLA2G4F -STXBP6 -RSPO1 -ADRB2 -HSPB3 -NPR1 -LDB2 -TACR3 -P2RY1 -CTNND2 -REPS2 -ITGAM -SIK2 -ADRA1B -FABP4 -PLA2G1B -OSCAR -S1PR1 -FPR2 -FPR1 -SOX7 -SIGLEC17P -GIMAP8 -PRKCE -SOSTDC1 -RXFP1 -PTGER4 -NMUR1 -PTCRA -RASGRP4 -KLF17 -AQP4 -SYNPO -MAL -FRMD3 -ID4 -TPSAB1 -MACROD2 -RCAN2 -IL16 -IL17D -COL6A5 -ABLIM3 -MMRN2 -NDNF -OLR1 -SULT1B1 -WFIKKN2 -SLCO4C1 -SLCO2A1 -LPL -A2M -CLEC14A -BDNF -NCKAP5 -FIBIN -SCN4B -CASKIN2 -NIM1K -CAVIN1 -ZBED2 -IL17RA -MYOZ1 -HTR3C -ZNF366 -SH2D4B -TMEM139 -GIMAP7 -C2orf71 -GATA2 -GPC5 -CDH5 -SERTM1 -PRF1 -TMEM64 -CHRM2 -AMIGO1 -RTKN2 -KCNA4 -NXPH3 -GRID1 -CADM1 -SPNS2 -MCEMP1 -FREM3 -GKN2 -LHFPL6 -OLFML1 -FAM162B -ST6GALNAC3 -CLDN5 -PRKD1 -SLIT3 -PROS1 -APOBR -ROBO2 -SLC24A3 -IL3RA -SFTPA2 -METTL7A -NRG3 -EVI2B -CD300LF -GLDN -ARHGAP30 -KANK3 -DCC -SPRY4 -TRPV2 -OVCH1 -PEAK3 -VWC2 -PRELP -PLAC9 -MAOA -SIRPB2 -MVB12B -KANK2 -GUCA2A -ADARB1 -C5AR1 -VEPH1 -GYPE -SPN -CFD -FAM49A -SULT1C4 -ARC -CCDC69 -PAPSS2 -COLGALT2 -ARHGEF15 -GRK5 -TGM2 -SAMD5 -CHIAP2 -C10orf128 -GPRIN2 -BMPR2 -HLA-DOA -NOTCH4 -AGER -CASP12 -MPIG6B -LILRB3 -AARD -MT1M -HBA1 -COL6A6 -GPX3 -TRGC1 -GIMAP1 -EMP2 -SEC14L6 -C20orf202 -LINC02471 -SMIM25 -LINC00092 -LHFPL3-AS2 -LINC01671 -C14orf132 -TRGC2 -TARID -HLA-DRB6 -HLA-DPA1 -LINC00702 -LANCL1-AS1 -MAGI2-AS3 -LINC00163 -SPAAR -NFAM1 -KIAA0040 -LINC00607 -LINC01936 -LILRA2 -CD302 -INMT -UPK3B -LINC02016 -ECEL1P2 -ETV5 -HBB -CEBPA -LINC00968 -SELENOP -MIR3945HG -PCDHA12 -PCDHGB7 -SIGLEC14 -TBX5-AS1 -NCAPGP2 -LINC02555 -PECAM1 -MYZAP -TXNIP -RASSF5 -GDF10 -PCAT19 -TBX2-AS1 -FENDRR -LINC01082 -LINC00551 -PCDHGB5 -DACH1 -GPIHBP1 -BANCR -PCAT14 -LINC00891 +FGR +PDK4 +SLC4A1 +CX3CL1 +CEACAM21 +SEMA3G +SLC6A13 +ANOS1 +ALOX5 +IL20RA +SLC11A1 +MARCO +FHL1 +EHD2 +HSD17B6 +ARHGAP31 +DAPK2 +MSR1 +ADRB1 +ARHGAP6 +CCDC85A +RASGRF1 +LIMCH1 +CHI3L2 +CALCRL +SPI1 +CLDN18 +MAOB +TGFBR3 +PTPN21 +RPS6KA2 +LMCD1 +CYBRD1 +LIMS2 +CD5L +FRY +ITGA8 +EDN1 +ITM2A +TNS1 +SESN1 +CPB2 +COL4A4 +CACNA1S +LRP2 +PILRA +CASS4 +SIGLEC1 +TBX5 +NOS1 +NLRC4 +JPH4 +DPYSL2 +FMO2 +SH2D3C +GADD45B +MFNG +PIK3IP1 +PDGFB +ANGPT4 +SIRPB1 +CCM2L +RS1 +VGLL1 +ACP5 +SGCG +RGCC +WFDC1 +FOXF1 +CA2 +CD37 +CLEC4M +PRX +SIGLEC5 +RASIP1 +CAV2 +CAV1 +HOXA5 +CPED1 +SLC1A1 +ENG +TYRP1 +PIP5K1B +PTGDS +PALD1 +VSIR +SPOCK2 +RGS9 +4-Sep +P2RX1 +SLC6A4 +SGCA +HLF +SLC16A6 +ODAM +WFS1 +SOD3 +CRYAB +SLC15A3 +VWF +SELPLG +LIN7A +ACSS3 +TNS2 +ART4 +C12orf49 +MDGA1 +BMP5 +FHL5 +KHDRBS2 +CLIC5 +NPR3 +HYAL1 +EFCC1 +ARHGEF26 +VIPR1 +TNNC1 +ACADL +EFEMP1 +HPCAL1 +EPAS1 +LEPR +PRG4 +NCF2 +ADGRL2 +FILIP1 +CNR1 +TCF21 +KLF9 +C1orf198 +FLVCR2 +LGALSL +DUSP1 +TEK +KCNJ5 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+SCUBE1 +ACE +LRRC36 +PTGIR +ABCG1 +JAML +PTH1R +FGFR4 +SIGLEC16 +CD300LG +NTNG1 +KCNT2 +C1orf115 +PKDCC +NOSTRIN +TGFBR2 +DNASE1L3 +CPA3 +CLEC3B +LRRC2 +KLF15 +EMCN +HHIP +ENPP6 +CITED2 +BMPER +KIAA1324L +FABP5 +SOX17 +SBSPON +GPR146 +CA3 +DCSTAMP +MAMDC2 +SVEP1 +FBP1 +VEGFD +OTUD1 +DEPP1 +C10orf25 +VSTM4 +JCAD +BTNL9 +CYYR1 +SYNPO2L +TMEM130 +MFAP4 +SCNN1G +MS4A7 +MS4A15 +TEF +DPEP2 +CA4 +GPD1 +KIR3DL1 +PPP1R14A +CD300C +FAM107A +CX3CR1 +CAVIN2 +AXIN2 +IL7R +WFDC12 +NPNT +ATOH8 +PLA2G4F +STXBP6 +RSPO1 +ADRB2 +HSPB3 +NPR1 +LDB2 +TACR3 +CTNND2 +ITGAM +ADRA1B +FABP4 +PLA2G1B +OSCAR +S1PR1 +FPR2 +FPR1 +SOX7 +SIGLEC17P +GIMAP8 +PRKCE +SOSTDC1 +RXFP1 +NMUR1 +PTCRA +RASGRP4 +KLF17 +AQP4 +SYNPO +MAL +FRMD3 +ID4 +TPSAB1 +MACROD2 +RCAN2 +IL17D +COL6A5 +MMRN2 +NDNF +OLR1 +SULT1B1 +WFIKKN2 +SLCO4C1 +SLCO2A1 +LPL +A2M +CLEC14A +BDNF +NCKAP5 +FIBIN +SCN4B +CASKIN2 +NIM1K +CAVIN1 +ZBED2 +MYOZ1 +HTR3C +ZNF366 +SH2D4B +TMEM139 +C2orf71 +GATA2 +GPC5 +CDH5 +SERTM1 +TMEM64 +CHRM2 +AMIGO1 +RTKN2 +KCNA4 +NXPH3 +GRID1 +SPNS2 +MCEMP1 +FREM3 +GKN2 +LHFPL6 +FAM162B +ST6GALNAC3 +CLDN5 +SLIT3 +PROS1 +APOBR +ROBO2 +SLC24A3 +IL3RA +SFTPA2 +METTL7A +NRG3 +GLDN +KANK3 +DCC +TRPV2 +OVCH1 +PEAK3 +VWC2 +PRELP +PLAC9 +MAOA +MVB12B +KANK2 +GUCA2A +C5AR1 +VEPH1 +GYPE +SPN +CFD +FAM49A +SULT1C4 +ARC +CCDC69 +PAPSS2 +COLGALT2 +ARHGEF15 +GRK5 +TGM2 +SAMD5 +CHIAP2 +GPRIN2 +HLA-DOA +NOTCH4 +AGER +CASP12 +MPIG6B +AARD +MT1M +HBA1 +COL6A6 +GPX3 +TRGC1 +GIMAP1 +EMP2 +SEC14L6 +C20orf202 +LINC02471 +SMIM25 +LINC00092 +LHFPL3-AS2 +LINC01671 +C14orf132 +TRGC2 +TARID +HLA-DRB6 +HLA-DPA1 +LINC00702 +LANCL1-AS1 +LINC00163 +SPAAR +LINC00607 +LINC01936 +LILRA2 +INMT +UPK3B +LINC02016 +ECEL1P2 +HBB +LINC00968 +SELENOP +MIR3945HG +PCDHA12 +PCDHGB7 +SIGLEC14 +TBX5-AS1 +NCAPGP2 +LINC02555 +PECAM1 +MYZAP +TXNIP +GDF10 +PCAT19 +TBX2-AS1 +FENDRR +LINC01082 +LINC00551 +PCDHGB5 +DACH1 +GPIHBP1 +BANCR +PCAT14 +LINC00891 \ No newline at end of file diff --git a/intro-pathway-analysis-visualization/lung.expr.entrez.gsea-full.xlsx b/intro-pathway-analysis-visualization/lung.expr.entrez.gsea-full.xlsx new file mode 100644 index 0000000..b8db1d8 Binary files /dev/null and b/intro-pathway-analysis-visualization/lung.expr.entrez.gsea-full.xlsx differ diff --git a/intro-pathway-analysis-visualization/lung.expr.up.txt b/intro-pathway-analysis-visualization/lung.expr.up.txt index 03ad813..6fe068b 100644 --- a/intro-pathway-analysis-visualization/lung.expr.up.txt +++ b/intro-pathway-analysis-visualization/lung.expr.up.txt @@ -1,383 +1,367 @@ -YBX2 -DLX6 -CELSR3 -PAX7 -SYT7 -ANLN -GABRA3 -ABCC2 -DEPDC1 -INSRR -ARNTL2 -HMGB3 -DEPDC1B -ZIC2 -MAGEC2 -POLQ -STYK1 -COL11A1 -SPAG4 -VMP1 -MCM10 -ASPM -PHKA1 -TRIP13 -HMMR -PPP2R2C -KCNQ2 -SPAG5 -UBE2T -FAP -RBFOX1 -PTPRH -NDC80 -NKAIN1 -IGSF9 -RAD54L -TMPRSS11E -PTHLH -DNMT3B -TPX2 -FER1L4 -BIRC5 -KIF4A -DLL3 -ORC6 -RGS17 -CDC6 -MMP11 -COCH -POLE2 -GINS1 -MYBL2 -PABPC1L -SALL4 -EEF1A2 -FERMT1 -FAM83D -SRPX2 -CENPI -RHBDL1 -SALL1 -OIP5 -MCM4 -FSD1 -MAST1 -STX1A -EZH2 -LHX2 -CA9 -EBF3 -DNAJC12 -GALNT7 -NEIL3 -NCAPG -KIAA1549L -FOXM1 -PRR4 -CDCA3 -TTK -POLR3G -ECT2 -CENPA -FHL2 -ABCB6 -RALGPS2 -AGMAT -SLC2A1 -CDC20 -NEK2 -CENPF -KIF14 -ATP10B -ONECUT2 -HELLS -TMEM156 -PAEP -TWIST1 -CENPK -STIL -HJURP -COL10A1 -WFDC3 -OR2B6 -C1orf61 -DLGAP5 -SYNGR3 -VIL1 -GNGT1 -PAICS -PPAT -ADM2 -BAIAP2L2 -VGF -E2F8 -EGLN3 -SGO1 -FAM155B -GINS2 -BARX1 -CA6 -TOP2A -RHBG -KHDC4 -FCRL2 -C1QTNF6 -CCNB1 -CDCA8 -TCN1 -ACRV1 -GOLM1 -PSAT1 -TROAP -B4GALNT1 -IGF2BP3 -BRIP1 -ARHGEF39 -TFAP2A -SLCO5A1 -SULF1 -KIF23 -KNL1 -ITPKA -BCL2L10 -CGREF1 -KIF11 -CEP55 -GPR87 -ADAMTS14 -DNA2 -CILP -CENPE -GCNT3 -PIF1 -FANCI -PMAIP1 -PLPP2 -SLC2A5 -PLK4 -KIF2C -NUF2 -FCRL5 -CRABP2 -KCNH1 -HHIPL2 -CDCA7 -DLX1 -CCDC150 -ABCA12 -TRPM8 -OCIAD2 -CCNA2 -LGSN -TPBG -ZC3HAV1L -FAM83A -CDKN2A -MKI67 -ADAM12 -CHEK1 -HMGA2 -SLC7A11 -CENPU -PDK1 -SPOCK1 -CABYR -EME1 -EPHB1 -MAGEC1 -SLC24A2 -CXCL13 -GLYATL2 -FBXO32 -BUB1B -TMEM171 -LRP8 -CCNB2 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