Merge branch 'master' of https://github.com/gladstone-institutes/Bioinformatics-Workshops

intro-pathway-analysis/ExampleData/lung.expr.dn.txt

@@ -0,0 +1,516 @@
+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
+CHRNA2
+PDLIM2
+TBX2
+TBX4
+PLBD1
+CAT
+FABP3
+CCRL2
+RAMP3
+GLIPR2
+HVCN1
+NECAB1
+C4BPA
+FAM124B
+MOCS1
+AHNAK
+EFNB2
+TMEM255A
+S1PR4
+RHOJ
+MASP1
+F2RL3
+MGAT3
+CGNL1
+CDO1
+STARD8
+USHBP1
+RGN
+COX4I2
+HIGD1B
+ADGRE3
+AOC3
+RAMP2
+TMEM204
+RAI2
+HSPA12B
+SSTR4
+MYH10
+KL
+PRAM1
+PDZD2
+GIMAP6
+LYVE1
+CNTN6
+GSTM5
+SORT1
+CD101
+ADAMTS8
+FAM189A2
+TBX3
+OASL
+CD36
+STX11
+CPM
+SLC19A3
+CYP27A1
+THSD1
+LMO7
+EDNRB
+SCN7A
+GYPC
+TMOD1
+RNF144B
+LRRC32
+FXYD6
+PAQR5
+SMAD6
+SEMA6D
+GCOM1
+DNASE2B
+RBP4
+PLA2G12B
+AOX1
+PRKG2
+FGF2
+ANXA3
+SLC39A8
+ERP27
+ACVRL1
+FBLN5
+CYP1A2
+ITGAX
+NKD1
+ABCA8
+GATA6
+SLC14A1
+PNMT
+SLC47A1
+FCN3
+C1orf162
+RXRG
+ADAMTSL4
+ZNF385B
+CNTN4
+CSRNP1
+STAC
+ADPRH
+AGTR1
+SLIT2
+NKD2
+HMGCLL1
+PRSS35
+AWAT2
+GPC3
+DOK2
+TACC1
+RSPO2
+PLIN2
+CDKN2B
+STOM
+ST8SIA6
+ANKRD1
+ESAM
+CLEC1A
+GPM6A
+HSPB8
+IGSF10
+SPARCL1
+UBASH3B
+ROBO4
+ABI3BP
+ANGPT1
+WNT3A
+FGD5
+GRIA1
+VSIG4
+AFF2
+ADAMTSL3
+TSPAN7
+TDRD9
+RAB11FIP1
+TSC22D3
+KCNJ15
+FAM46B
+SHROOM4
+ITLN2
+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

intro-pathway-analysis/ExampleData/lung.expr.up.txt

@@ -0,0 +1,367 @@
+YBX2
+DLX6
+CELSR3
+PAX7
+SYT7
+ANLN
+GABRA3
+ABCC2
+DEPDC1
+INSRR
+ARNTL2
+HMGB3
+DEPDC1B
+ZIC2
+MAGEC2
+POLQ
+STYK1
+COL11A1
+SPAG4
+MCM10
+ASPM
+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
+FSD1
+MAST1
+STX1A
+EZH2
+LHX2
+CA9
+EBF3
+DNAJC12
+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
+PPAT
+ADM2
+BAIAP2L2
+VGF
+E2F8
+EGLN3
+SGO1
+FAM155B
+GINS2
+BARX1
+CA6
+TOP2A
+RHBG
+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
+ZC3HAV1L
+FAM83A
+CDKN2A
+MKI67
+ADAM12
+CHEK1
+HMGA2
+SLC7A11
+CENPU
+PDK1
+SPOCK1
+CABYR
+EME1
+EPHB1
+MAGEC1
+SLC24A2
+CXCL13
+GLYATL2
+FBXO32
+BUB1B
+TMEM171
+CCNB2
+DPYSL5
+XDH
+HIST1H2BD
+CDC25C
+HIST1H4H
+CILP2
+TFF1
+RECQL4
+SPC24
+TEDC2
+AK4
+AKR7A3
+KIF26B
+LINC01116
+TRIM46
+TSACC
+CRYBA2
+AIM2
+KIF15
+MAD2L1
+IL31RA
+STEAP1
+SP8
+CTHRC1
+MELK
+TSHR
+PGM2L1
+SLC16A9
+GJB2
+SKA3
+E2F7
+GLB1L3
+GPT2
+PPP1R14D
+NETO1
+HTR3A
+PLK1
+GREM1
+TTYH1
+KLK6
+RAB26
+PBK
+COL3A1
+GDNF
+SOX14
+RAB3B
+COL22A1
+CKAP2L
+BUB1
+ONECUT1
+CDK1
+CST1
+HOXB9
+HS6ST2
+P2RY6
+RRM2
+FRMD5
+C5orf34
+FUT9
+MYEOV
+SYT12
+C11orf86
+MUC13
+SPTBN2
+NWD2
+EXO1
+ANKRD36C
+IL20RB
+LEP
+UBE2C
+MARCKSL1
+ANKS4B
+RMI2
+ETV4
+FAM172BP
+GPX2
+ATAD5
+FUT2
+CD19
+DNAJC22
+CPNE7
+ANKRD18A
+EMC3-AS1
+NQO1
+B4GALNT4
+GALNT9
+PYCR1
+EPHA10
+IQGAP3
+KNTC1
+POU3F2
+CDCA2
+PARPBP
+PRAME
+DNAH14
+KIF18B
+SAPCD2
+THBS2
+HPDL
+ERCC6L
+TNFRSF18
+TMPRSS11A
+BAGE2
+HIST1H1C
+ENTPD8
+ATP2A1
+XRCC2
+HIST1H2AI
+S100A2
+HIST1H2AG
+HIST1H2AD
+SCN8A
+HIST1H4C
+DMBX1
+PRB3
+AKR1B10
+EPS8L3
+ARHGAP11A
+SNORA73B
+SNORA23
+ZYG11A
+LINC01270
+IGFL2
+FAM83A-AS1
+LGR4
+AKR7L
+IGHG4
+IGHG1
+PPP1R14BP2
+GPC2
+LINC02418
+VAC14-AS1
+UBE2QL1
+TNFRSF25
+LINC01983
+HAGLROS
+PSMD10P2
+AKR1B15
+LINC02474
+NKX1-2
+ANKRD36BP2
+FEZF1-AS1
+FOXD3-AS1
+DLX6-AS1
+LINC00665
+LINC01271
+LINC02535
+DSCAM-AS1
+RPSAP52
+CCDC169
+MNX1-AS1
+RPL18P13
+LINC00461
+LINC02014
+LUCAT1
+LINC02362
+LINC01234
+LINC00942
+PVT1
+SCARNA13
+BBOX1-AS1
+MEX3A
+LINC00346
+SALL3
+TUBB3
+LINC02544
+VPS9D1-AS1
+LINC01977
+RUNDC3A-AS1
+AFAP1-AS1
+LHX1
+UHRF1
+HIST1H2BF
+NEFL
+RDM1
+HIST1H2AM
+LINC01395
+HELLPAR
+SNHG4

intro-pathway-analysis/README.md

@@ -0,0 +1,5 @@
+# Pathway Analysis Online
+
+[Link to wiki](https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki/Introduction-to-Pathway-Analysis-and-Visualization)
+
+### Description of files