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*.cys filter=lfs diff=lfs merge=lfs -text *.cys filter=lfs diff=lfs merge=lfs -text
*.cluego filter=lfs diff=lfs merge=lfs -text *.cluego filter=lfs diff=lfs merge=lfs -text
*.tsv filter=lfs diff=lfs merge=lfs -text *.tsv filter=lfs diff=lfs merge=lfs -text
*.pdf filter=lfs diff=lfs merge=lfs -text
Day_1/GO_course_2020-Day1.pdf 0 → 100644 LFS
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Day_2/2020_Ontologies_p1_Cytoscape.pdf 0 → 100644
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Day_2/Day_2_Enrichment_Analysis.pdf 0 → 100644
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Day_2/Exercises_and_Tutorials/0.Tutorial/base_nets.cys 0 → 100644 LFS
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Day_2/Exercises_and_Tutorials/0.Tutorial/network_0.5_id_list.txt 0 → 100644
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Ensembl:ENSG00000126602
Ensembl:ENSG00000130726
Ensembl:ENSG00000138430
Ensembl:ENSG00000163161
Ensembl:ENSG00000166598
Ensembl:ENSG00000175595
Ensembl:ENSG00000182473
Ensembl:ENSG00000112335
Ensembl:ENSG00000112062
Ensembl:ENSG00000125740
Ensembl:ENSG00000175387
Ensembl:ENSG00000177606
Ensembl:ENSG00000184708
Ensembl:ENSG00000103657
Ensembl:ENSG00000105851
Ensembl:ENSG00000116473
Ensembl:ENSG00000139842
Ensembl:ENSG00000143622
Ensembl:ENSG00000144566
Ensembl:ENSG00000145604
Ensembl:ENSG00000159069
Ensembl:ENSG00000165699
Ensembl:ENSG00000166851
Ensembl:ENSG00000167986
Ensembl:ENSG00000187608
Ensembl:ENSG00000187840
Ensembl:ENSG00000198793
Ensembl:ENSG00000108669
Ensembl:ENSG00000185344
Ensembl:ENSG00000119689
Ensembl:ENSG00000136271
Ensembl:ENSG00000169764
Ensembl:ENSG00000115942
Ensembl:ENSG00000179632
Ensembl:ENSG00000147614
Ensembl:ENSG00000159720
Ensembl:ENSG00000173638
Ensembl:ENSG00000115233
Ensembl:ENSG00000125676
Ensembl:ENSG00000147416
Ensembl:ENSG00000176974
Ensembl:ENSG00000182199
Ensembl:ENSG00000183207
Ensembl:ENSG00000278535
Ensembl:ENSG00000171453
Ensembl:ENSG00000118640
Ensembl:ENSG00000124333
Ensembl:ENSG00000116830
Ensembl:ENSG00000175054
Ensembl:ENSG00000177302
Ensembl:ENSG00000187790
Ensembl:ENSG00000253729
Ensembl:ENSG00000120438
Ensembl:ENSG00000135624
Ensembl:ENSG00000146701
Ensembl:ENSG00000150753
Ensembl:ENSG00000163468
Ensembl:ENSG00000166226
Ensembl:ENSG00000169679
Ensembl:ENSG00000213347
Ensembl:ENSG00000120586
Ensembl:ENSG00000156958
Ensembl:ENSG00000168906
Ensembl:ENSG00000148926
Ensembl:ENSG00000164619
Ensembl:ENSG00000204531
Ensembl:ENSG00000163485
Ensembl:ENSG00000172732
Ensembl:ENSG00000241258
Ensembl:ENSG00000138071
Ensembl:ENSG00000138346
Ensembl:ENSG00000141367
Ensembl:ENSG00000148225
Ensembl:ENSG00000154767
Ensembl:ENSG00000155959
Ensembl:ENSG00000170950
Ensembl:ENSG00000171865
Ensembl:ENSG00000175792
Ensembl:ENSG00000196236
Ensembl:ENSG00000204628
Ensembl:ENSG00000255767
Ensembl:ENSG00000132781
Ensembl:ENSG00000133460
Ensembl:ENSG00000134899
Ensembl:ENSG00000135446
Ensembl:ENSG00000135679
Ensembl:ENSG00000136856
Ensembl:ENSG00000140398
Ensembl:ENSG00000140451
Ensembl:ENSG00000142583
Ensembl:ENSG00000143384
Ensembl:ENSG00000143476
Ensembl:ENSG00000144554
Ensembl:ENSG00000145649
Ensembl:ENSG00000146411
Ensembl:ENSG00000146414
Ensembl:ENSG00000147889
Ensembl:ENSG00000151229
Ensembl:ENSG00000153147
Ensembl:ENSG00000153487
Ensembl:ENSG00000157703
Ensembl:ENSG00000160200
Ensembl:ENSG00000160326
Ensembl:ENSG00000163393
Ensembl:ENSG00000163581
Ensembl:ENSG00000166803
Ensembl:ENSG00000167513
Ensembl:ENSG00000169188
Ensembl:ENSG00000170734
Ensembl:ENSG00000173262
Ensembl:ENSG00000177889
Ensembl:ENSG00000178295
Ensembl:ENSG00000181163
Ensembl:ENSG00000181856
Ensembl:ENSG00000197241
Ensembl:ENSG00000197496
Ensembl:ENSG00000273604
Ensembl:ENSG00000274276
Ensembl:ENSG00000134365
Ensembl:ENSG00000150337
Ensembl:ENSG00000160712
Ensembl:ENSG00000228321
Ensembl:ENSG00000155827
Ensembl:ENSG00000149532
Ensembl:ENSG00000173207
Ensembl:ENSG00000198242
Ensembl:ENSG00000168509
Ensembl:ENSG00000159479
Ensembl:ENSG00000231135
Ensembl:ENSG00000214960
Ensembl:ENSG00000163682
Ensembl:ENSG00000163947
Ensembl:ENSG00000165629
Ensembl:ENSG00000173848
Ensembl:ENSG00000196497
Ensembl:ENSG00000257315
Ensembl:ENSG00000164287
Ensembl:ENSG00000164733
Ensembl:ENSG00000166974
Ensembl:ENSG00000168291
Ensembl:ENSG00000177000
Ensembl:ENSG00000182521
Ensembl:ENSG00000185813
Ensembl:ENSG00000242247
Ensembl:ENSG00000259371
Ensembl:ENSG00000188779
Ensembl:ENSG00000174125
\ No newline at end of file
Day_2/Exercises_and_Tutorials/0.Tutorial/network_0.5_id_list_symbols.txt 0 → 100644
View file @ 9dba6ab6
CDK2
DNAJA3
TOP3B
THOC2
RNF40
FOLR1
SLC22A2
RFC1
EIF4ENIF1
PICK1
MAPK1
VAMP7
PCYT2
GLG1
HSP90AA1
XRCC1
MUS81
SORL1
CDK1
MAP3K7
CDH1
FBXO5
DOT1L
ERCC2
DNAJC3
PIK3CG
PGM1
DOHH
KIF22
SPECC1L
GIPC1
TBP
BUB1
RAD51
TTF2
CCT5
NUP155
BRCA2
MAD1L1
FOXH1
REST
APMAP
TBPL2
LRP1
RBX1
CPSF7
HERC1
HOXD13
PES1
PGAM5
CUL4A
PDLIM7
RNASEH1
ZBTB24
SRCAP
RAD17
EMC7
PHF21A
HMGA1
BAZ2A
DLAT
CTSD
BMP5
CALR
NCAPD3
RPA2
ASH1L
IL6R
ECHS1
PGK1
PRDX5
WDR31
H0YFU0_HUMAN
UGP2
MAPK14
MED8
RNF7
POLD2
VCP
IFT52
BMP4
GLYR1
IGF2R
BMP7
ISOC2
RAE1
UTP20
PIK3CB
POLH
HSP90AB1
WRN
SLC2A4
SYP
FCN1
DKK3
HFE
CPS1
STAB2
GART
HSP90B1
APLF
OLA1
TLR2
LEF1
SYF2
MTHFR
RPS8
POLD3
UBE2C
MLL3
GREM2
KCTD10
CCT2
GRPEL2
ANAPC10
CDC20B
CCT4
DNA2
FCGR1A
CDC26
TGFB1
RGN
NCAPG
FZR1
ATR
SLC11A2
CYTH2
TP53
PIAS1
EEA1
LBP
TRIM28
WDFY1
DDX56
TMEM135
CALCRL
PGK2
BMPR1B
SCARF1
WDFY2
ARFGAP3
MSH2
USF2
SMC1B
HAMP
OBFC1
ENG
SMAD4
HFE2
TBC1D22A
MBL2
ZFYVE16
LRP3
VAMP8
DNAJC13
TFRC
ANAPC2
CCR2
RAB7A
FFAR2
MAF1
MLL4_HUMAN
CHTF18
USP8
ERCC3
PSMD14
ACVRL1
SRSF6
MAP2K7
BLM
CRCP
SMAD2
POLA2
LIG1
CDT1
SLC30A4
TSC1
SLC22A15
PIF1
MAT1A
RPA4
SLC2A13
RNF20
FBXW5
CSTF3
ATP5B
BOD1L1
DDB1
PSMC4
ACVR1
ANAPC11
VBP1
TOP2A
ERCC1
TOP3A
DLG1
RPL23A
POLD4
SNX1
TSC2
LRP1B
GPI
MAD2L1
SKOR1
MALSU1
VPS33B
SRSF4
RAP1A
RIT1
TLR3
SYNJ1
F2RL2
HDAC1
SETBP1
ERCC4
SLC2A7
SMURF2
DVL1
TTI2
BRCA1
ADORA1
UBE2N
CDC27
XPC
SLC2A10
TFR2
BMPR1A
COG4
EXO1
ANAPC4
AP1G1
SIRT1
RAD23B
GADD45G
ACTL8
ATP5A1
TLR1
AHCTF1
GALK2
IPO4
MTOR
ARFGAP2
PCNA
TCF3
C9orf85
CPSF6
CCT3
NSF
MAPRE2
SLC2A2
ZRANB3
OTC
ACVR2A
MSH6
SLC2A1
FANCM
PLK1
CDC20
CHRDL1
CORO1C
TOP2B
RAD52
LRP2
LPL
PAPD7
CCT8L2
NCAPG2
HLTF
SLC2A14
RFC2
SSBP1
SKI
UBE2D1
NEIL1
CLTC
PLAU
CLPB
GNB2L1
ZBED6
MAT2A
SHMT2
ATP6V0A2
SKP2
MAPRE3
PMS1
ATP6V1B1
CLTCL1
DLG3
MUTYH
XPNPEP3
ANAPC1
RUVBL1
ATP5C1
TADA2B
BUB1B
SVOPL
SERPINE1
HGS
ACTR2
CAD
TCP1
PNN
APEX1
MAP2K3
ALDH18A1
SLC2A5
PIGM
ITSN1
RPL9
MDH2
DLST
MLH3
JUN
MXD3
ADORA2A
SMAD3
GRPEL1
KPNB1
CYTH1
AP1S1
MRC1
RPLP0
GDF9
MSH4
CKS2
FSTL1
APC
GAPDH
VPS35
ERBB2IP
NCAPD2
PGM5
MRPS33
ISPD
GALK1
ING1
RAMP2
AADAT
SMAD9
PSMC1
UBE2D3
PMS2
PRM1
SHMT1
NCAPH2
IFNG
FH
ANAPC5
FANCD2
RPA3
HOXA13
GREM1
KIAA0101
GZMA
EIF4EBP1
AHSA2
AMPH
SMARCA5
STK11
N4BP2
PSMD1
TOR1A
BMPER
TPR
ANAPC13
BUB3
CDC23
SMC2
SLC2A9
VEGFA
CTSB
RAB5A
BAMBI
DTL
APEX2
PDS5B
ADM
POLD1
WDR76
CKS1B
CRP
SMURF1
SFTPD
SMC4
SMC1A
ISG15
RABEPK
UBE2S
DLD
XPA
PRUNE
SNIP1
MECP2
UQCRC1
BAZ1B
MBD4
M6PR
RFC5
RPS20
BMP6
E2F1
PRKG1
DMC1
SNX2
EGFR
CX3CL1
ATP6V0D2
ZNF207
RAMP3
BMPR2
MLL
CDC16
NPM1
ERCC5
CCT7
NBL1
CDKN1A
SHPRH
SLC2A12
PHF5A
MCL1
EXOC7
AHDC1
DCAF11
RPL12
CER1
TPT1
DERL1
SMAD6
ATP6V0D1
ANAPC7
UBE2E1
RPA1
PICALM
FCN2
TLR4
RFC3
PSMC5
EPRS
DGKQ
RAB34
BAX
PI4KB
NOG
BMP2
ZBED4
SLC19A1
PDHB
SLC2A11
NTHL1
SLC2A8
RUVBL2
SLC2A3
SLC2A6
TRAP1
NCAPH
CBS
PAPD5
CDKN2A
HMGA2
POLR1C
LIG3
SNX3
PRKDC
SMAD1
USF1
FBXO22
PPTC7
ARHGEF3
MDM2
AHSA1
FOSB
TF
WRNIP1
STAB1
COPS5
POU5F1
ATP6V1B2
MYC
PMPCB
SNX4
MLH1
ZNF524
NDC80
HSPD1
UNG
MSH3
SMAD7
SMC3
CD14
NET1
MGP
CALR3
NRP1
ORC2
CFHR4
279594
ACVR2B
MCPH1
MAPK3
GEN1
CCT8
FEN1
PATZ1
POR
DNAJC7
CDK4
PRC1
SMAD5
ISOC1
RFC4
TBC1D22B
Day_2/Exercises_and_Tutorials/0.Tutorial/sgd_list_exercise.txt 0 → 100644
View file @ 9dba6ab6
CRM1
SRM1
GCN3
NIP7
GSP1
HRP1
TEF2
TIF35
YEF3
MAD2
\ No newline at end of file
Day_2/Exercises_and_Tutorials/1.BinGO_PinGO_ClueGO_EnrichmentMap/ClueGO_with_background/id_list.txt 0 → 100644
View file @ 9dba6ab6
EntrezGene ID GeneName
51703 ACSL5
94 ACVRL1
211 ALAS1
23092 ARHGAP26
9459 ARHGEF6
55589 BMP2K
1234 CCR5
253175 CDY1
9085 CDY1
203611 CDY1
9426 CDY1
253175 CDY1B
9085 CDY1B
203611 CDY1B
9426 CDY1B
203611 CDY2A
9426 CDY2A
253175 CDY2A
9085 CDY2A
203611 CDY2B
9426 CDY2B
253175 CDY2B
9085 CDY2B
9620 CELSR1
101928723 CHD5
26038 CHD5
1131 CHRM3
1138 CHRNA5
1259 CNGA1
10699 CORIN
1359 CPA3
1472 CST4
10800 CYSLTR1
2191 FAP
2213 FCGR2B
54328 GPR173
338442 HCAR2
57657 HCN3
9146 HGS
8518 IKBKAP
3559 IL2RA
10994 ILVBL
3619 INCENP
10788 IQGAP2
3704 ITPA
4058 LTK
4063 LY9
4216 MAP3K4
5871 MAP4K2
4593 MUSK
83463 MXD3
91807 MYLK3
8386 OR1D5
5122 PCSK1
5833 PCYT2
5142 PDE4B
5213 PFKM
11284 PNKP
5430 POLR2A
5510 PPP1R7
5523 PPP2R3A
5531 PPP4C
5538 PPT1
85481 PSKH2
11251 PTGDR2
10076 PTPRU
25945 PVRL3
51762 RAB8B
64080 RBKS
8607 RUVBL1
122042 RXFP2
89777 SERPINB12
6494 SIPA1
8877 SPHK1
7980 TFPI2
112858 TP53RK
7179 TPTE
51175 TUBE1
5756 TWF1
Day_2/Exercises_and_Tutorials/1.BinGO_PinGO_ClueGO_EnrichmentMap/EnrichmentMap/12hr_topgenes_source.txt 0 → 100644
View file @ 9dba6ab6
ZNF259 C13orf3 CA12 SUSD3 OLFML3 NPNT BCL2L11 PUS1 MCM10 BTG2 TXNRD1 IL1RAP ASB9 TSEN2 PRSS23 PPAN BAMBI LOC93622 NPY1R LOC283551 EGR3 Magmas DAB2 SLC3A2 SLC2A10 WFS1 RAB31 MYB MRPS17 PRMT5 MYADM DGAT2 GEM ARMCX6 PGR FAM60A C21orf59 HOMER3 PPP1R3C S100A7 ID1 SLC19A2 NUDCD1 TARP PGLYRP2 BOP1 FKBP4 PSCA FAM46A SNX7 SLC7A5 MYBL1 PDLIM3 SLC2A1 BTG1 KYNU HSPB8 C12orf24 HIG2 BLNK SGK3 PCYOX1L ABCG1 PMP22 DYNLRB1 NOLC1 LOC645722 C9orf89 HARS REEP5 MAK16 TMEM48 DYNLT3 PRPF4 BAG2 ITGB6 PPIF TOMM6 IMPA2 ABAT PTGES RET OGFOD1 GRSF1 TMEM164 AREG MYO1B CAB39L SLC25A15 ORAI3 CYB5R1 TNS3 ARRDC4 PA2G4 BIK DRAM POLR3H CCDC85B CLMN ARMC10 PTP4A1 CXCL12 TP53INP1 ZDHHC7 ELOVL5 RBL2 DDX21 HSPC111 COMMD3 UTP18 SYTL5 IARS IGFBP4 DOK7 BCL2L1 C12orf66 UGT1A1 TMEM135 TRGC2 CRELD2 KLHDC2 SLC1A4 LXN TUFT1 SLC26A2 CCNG1 GEMIN4 RCL1 NP UGT2B15 MRPL15 SLC7A1 ENO1 GPATCH4 CEP78 PLLP PKIB SLC16A6 TRAM2 C20orf3 SLC9A3R1 FGF13 WDR3 SRM ATP6V1D EFNA1 NRBP1 TMEM194A PTRH2 SSR3 PAICS CAT CCNG2 TSKU SC4MOL PIK3R3 MLF1IP GRB14 CYBASC3 TMEM59 CELSR2 IL20 C15orf48 SFRS7 SIAH2 DSCC1 LOC100130886 HOXC13 GEMIN5 ANKH EIF2B2 CDC7 CDKN2B KIAA1522 RAF1 FAM84B TMED8 SLC16A1 FLJ13137 PDZK1 FLJ41603 PYCRL CTNND1 NEDD9 CHCHD10 S1PR3 MXD4 SVIL DPH2 MRPL16 STX12 C8orf32 ZDHHC8 WSB2 OTUD6B C1orf163 TIPARP RHOQ RFX5 FAIM3 SSBP1 LHX1 PPP6C PNO1 UTP6 DNTTIP2 RPN1 ITPRIPL2 WDR21A MREG PPM1E YPEL2 SGCG SIDT2 SOX3 ATP8B2 C10orf2 CACYBP MRPS2 BXDC1 KLF10 LDLRAD3 NUP107 ARID5B CDC123 NLN TIPIN TET2 RASGRP1 WBP1 TPD52L1 MAGOHB C14orf138 WDR75 C19orf48 RAPGEF2 NOC3L EIF3J CLDN4 FLJ11151 TPBG DEPDC6 MRTO4 RRP15 STARD10 RNF126 UBXN8 SRPRB NUDT7 BCAS1 MAP2K1IP1 SLC12A2 POLR3K WDR12 HBP1 UTP15 CCDC147 MAP1LC3B NCL LOC541471 NR3C1 GREB1 RRS1 PDXP FOXP1 CCT4 MCM6 WBSCR22 MBP HEBP1 CFL2 DDIT4 ABCA3 BCS1L C3orf26 TMEM38B OTUD7B ASB13 AKR1C2 LONRF2 GLA FDX1L LOC729013 RHOD ID3 SEH1L NR5A2 PTP4A2 BLVRB RBM24 TMEM49 RAN EXOSC2 KIFAP3 ANK3 FASTKD2 PPFIBP2 ABCE1 CREB3L4 NTN4 QSOX2 IGF2R DUSP10 SLC15A4 UTP20 GCNT1 KIAA1804 FAM83A STC1 LOC729680 RUSC1 NEIL2 CLN6 TBX2 GAL NDP UGDH ELOVL2 MANEAL FOSL2 PMAIP1 TRABD VPS37A CTA-221G9.4 IGSF3 PPM1K TIMM17A HOTAIR PRAGMIN LMCD1 KLF9 C2orf55 KCNK6 FER1L3 NRIP1 ZNF766 YPEL5 IL1R1 TMEM138 LITAF TSC22D3 FLNB NOC2L UGT1A3 MARK2 NAT10 SMS NARS2 KIAA1609 LOC100128881 EXOSC9 ERBB2 NSMCE2 POLR2D CCDC86 TMEM97 CTSD MITF TACC1 PTK6 SLC25A32 TMEM126B ZFP36L2 TLE1 TYRO3 CCT3 TMPRSS3 MRPS23 HIST3H2A BRI3BP TGFBI PWP2 SOCS2 FAM84A RILPL2 MFSD11 NME7 FBXL6 NUMA1 ILF3 METTL1 RFTN1 NOL14 GPC6 GPD1L PNPT1 MOCS2 ACAA2 KIAA0020 RELL1 PMPCB TGFA TIMP3 RAB5B C15orf57 PDSS1 THOC5 NXT1 SDF2L1 GADD45B DHX33 LRRC1 MRPL36 TJP2 CSE1L PRMT1 PHB2 COL12A1 FLJ20021 JPH1 CIRH1A SLC25A25 APPL2 EIF2S1 IFNA21 SNRPD3 FAM107B MRFAP1L1 LOC374443 CCDC53 COMT PISD PODXL TMEM64 FABP5 WWC1 UCHL5IP POLDIP2 MCM2 RIOK1 IFT20 AUP1 ERBB3 LMBRD1 ENPP1 VPS13B GPR77 AQP3 GALNAC4S-6ST SIPA1L1 MRPL3 MCC CCDC58 UCK2 AGPAT5 GCH1 SLC25A33 CYP2R1 TRNT1 LOC26010 OSMR MAFF RWDD2A MGP HMGCL IFRD2 LAMP1 RPA2 SH3BP5 MRPS12 PXMP4 NAV2 CSTA PTRH1 PRR15 SLC25A19 SPINK4 CARS EFCAB4B RAB3GAP1 TGIF2 FGFBP2 STOM HSPA9 CCT2 MTMR1 PUS7 DLEU1 UGT1A6 ARNT2 WDR74 ADM DNAJC1 ULBP2 CD3EAP DDEFL1 GOLSYN UMPS BAG5 C9orf142 KRT19 LOC100132684 LOC100132999 LYAR AGR3 IMAA KIAA0831 YPEL3 WDR77 PRDM6 ABCA12 DHRS2 CHAF1A FEN1 MYEOV2 IDH1 MYC NOB1 DUS3L EEF1E1 MAP1B GPN3 HARBI1 SYTL2 ORC1L ST8SIA4 ST3GAL4 RHBDF1 LOC375190 RABGAP1 C3orf14 CAP1 OPTN BOK OLFM1 MLXIP C2orf64 GART IGFBP3 CAB39
\ No newline at end of file
Day_2/Exercises_and_Tutorials/1.BinGO_PinGO_ClueGO_EnrichmentMap/EnrichmentMap/24hr_topgenes_source.txt 0 → 100644
View file @ 9dba6ab6
CA12 FAM171B CELSR2 RFTN1 SOCS2 IL1R1 NPTN IL20 LXN SLC16A1 PDZK1 PPP1R3C ESR1 FDFT1 DRAM CRIM1 BAMBI ADM GPR160 HIST1H3H TP53INP1 MYC COLEC12 CAT NOC3L TWSG1 PRELID1 RBM24 IGSF3 OLFML3 SUMF2 GEMIN5 IMP4 RANBP1 BTG2 B3GNT5 NPNT PRSS23 SUSD3 SLC3A2 MRPL15 RAB27B FARSB NTN4 TUBB6 SRPR BCAS3 DGKH SRM SLC12A2 UBA5 BIK ANK3 SEPP1 YPEL3 EPHA4 DGAT2 FAM84A ARNT2 PLA2G10 SIAH2 IGFBP3 TSC22D3 HSPB8 DCTN4 FLJ12993 RPP40 RHBDF1 ID2 SLC26A2 LOC441046 GBP3 LOC100133182 CTSD C20orf7 AUH CHSY1 RUVBL1 UBE2T SPAG5 LYAR GALNT12 LHFP IARS AKR1C3 SYNGR3 TIPARP S100A7 FKBP4 SEL1L FAM84B ZNF26 WWOX PTPN18 RTN2 SSBP2 RNF144B C12orf31 RBL2 LOC100130886 PTPRJ TSPYL4 PTP4A1 CCNB1 LRRC59 SLC7A5 TIMM8A TMEM83 MAP1LC3B CDR2 IHPK2 VAMP8 RAP1GAP TPBG DHRS2 SASH1 DNAJB11 FGF13 PLEKHF2 TMEM135 BLNK NAT10 CCT4 EGR3 PKIA NAV2 WDR21A DAB2 PHB HIG2 TFPI CXCL12 FABP5 TMPRSS3 AREG MYBL1 PSMD3 ACPP CXCR7 MBTPS2 C1orf149 GLA SPINK4 CCNG2 MRPS6 CREB3L4 PPME1 C12orf45 KCNK6 SGSM2 NLE1 JAK2 PRPF4 CLU MTHFD1 THRSP PMP22 EMG1 GSTM3 YPEL2 REEP5 EPB41L4A TMEM49 PNPT1 RPS26 NDUFAF2 DDX17 PNO1 ABCG1 NME1 LOC374443 CRISPLD2 TPD52L1 NPY1R HMCN1 ERBB3 MRPS25 PPFIBP2 MYO1B CANT1 SNAP23 ETNK2 MRPS17 ITPRIPL2 PTPLA HSPC111 RBM28 NQO1 FAM174B COBL RRP15 PRMT5 BCAS1 GAL FJX1 GLO1 TSPAN1 LITAF TMEM150 CORO1B PDCD2L ZNHIT6 CTSA B3GALNT2 DDIT4L HAX1 SH3YL1 CD164 DKK1 MYO6 METTL1 TUFT1 ST8SIA4 TLE1 ACSF2 GADD45B GPATCH4 PDLIM3 CRBN CORO2A RET LOC113230 SH3BGRL CHCHD4 SAT1 PLK1 GEMIN6 FHL2 DHRS12 DCN SLC20A2 ALDH1B1 RHOBTB1 UGT2B15 C2orf55 TXNDC5 NXF1 TMEM164 CDCA8 CTNNB1 APPL2 GOT1 ANO6 SCARB2 ERBB4 ZFP36L2 CEACAM6 LASS2 EIF2B3 IGFBP5 DARS2 BOLA2 RILPL2 HSP90AA1 CDCA5 ECH1 FAM102B PSMF1 ABCC5 AHSA1 MORC4 LTV1 ARHGAP5 MKI67IP FAM3B EFNA1 EPS8 SYTL5 SH3BGRL2 EHBP1 LAMP2 SNRPC PBXIP1 NPR3 MRPL16 POLR3H TMEM106C TMEM32 SLC1A1 PLSCR3 ZWILCH PEG10 GPR89B TCF7L2 SYTL2 TADA3L PPM1K DPH2 STX12 DDX10 DENND1A EIF4A1 YPEL5 SCCPDH PP14571 PRR5 COBLL1 STK17A FAM110C SPDEF RAB26 VKORC1 PXMP4 PODXL MXD4 TRGC2 GPX3 PPIF LRP8 RWDD2A SERPINB1 C1orf115 ARMC10 DNAJC2 TMEM59 EFCAB4B ID4 RIN2 COQ3 SOX3 WDR75 C12orf66 FAM107B LIMA1 MB MBNL2 GPR109B DDX56 DDIT4 UBE2S UGT2B17 SERPINA3 FLJ35776 WDR12 RAB2A LOC440957 MRPL14 CCDC138 OGFOD1 TGFBI ETFA BLMH MEST C19orf10 C3orf31 SAMD12 VPS37C NPM3 AURKA GRB14 PGM5 CENPA ATP8B1 WDR4 MRPL3 NNT GATA3 RP1-21O18.1 ASB9 BTG1 SNRPD3 TACSTD2 PSMB5 ARL6IP5 C14orf4 DOK7 ADORA1 PTPLAD1 TOP2B KIAA0114 PITPNA C1QBP ANAPC7 TM9SF2 EFEMP1 GCLM SPSB3 ADIPOR2 BUB3 MANEAL ID3 PTS SFRS7 ASCL1 SGK3 NP FLAD1 HBP1 PGR WDSOF1 ATP5G1 MRPS12 PTCD3 AGXT2L2 ASNSD1 APPBP2 ID1 ITGB5 NUDCD1 PAWR FLJ41603 CEP55 ZC3H15 TIMM17A PSD3 PRICKLE4 ARHGAP8 DEPDC6 DNAJC1 RMND5B GRN CLEC2D PSMD12 SPCS3 FOXC1 CDCA7 FUT8 MYEOV2 POLR2F FHL1 BOP1 F11R CNP DTYMK ASS1 IRX2 LOC100133166 SLC2A1 THBS1
\ No newline at end of file
Day_2/Exercises_and_Tutorials/1.BinGO_PinGO_ClueGO_EnrichmentMap/base_nets.cys 0 → 100644 LFS
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File added
Day_2/Exercises_and_Tutorials/2.ReactomeFI_tutorial/gene_symbols_for_net_0.5_source.txt 0 → 100644
View file @ 9dba6ab6
CDK2
DNAJA3
TOP3B
THOC2
RNF40
FOLR1
SLC22A2
RFC1
EIF4ENIF1
PICK1
MAPK1
VAMP7
PCYT2
GLG1
HSP90AA1
XRCC1
MUS81
SORL1
CDK1
MAP3K7
CDH1
FBXO5
DOT1L
ERCC2
DNAJC3
PIK3CG
PGM1
DOHH
KIF22
SPECC1L
GIPC1
TBP
BUB1
RAD51
TTF2
CCT5
NUP155
BRCA2
MAD1L1
FOXH1
REST
APMAP
TBPL2
LRP1
RBX1
CPSF7
HERC1
HOXD13
PES1
PGAM5
CUL4A
PDLIM7
RNASEH1
ZBTB24
SRCAP
RAD17
EMC7
PHF21A
HMGA1
BAZ2A
DLAT
CTSD
BMP5
CALR
NCAPD3
RPA2
ASH1L
IL6R
ECHS1
PGK1
PRDX5
WDR31
H0YFU0_HUMAN
UGP2
MAPK14
MED8
RNF7
POLD2
VCP
IFT52
BMP4
GLYR1
IGF2R
BMP7
ISOC2
RAE1
UTP20
PIK3CB
POLH
HSP90AB1
WRN
SLC2A4
SYP
FCN1
DKK3
HFE
CPS1
STAB2
GART
HSP90B1
APLF
OLA1
TLR2
LEF1
SYF2
MTHFR
RPS8
POLD3
UBE2C
MLL3
GREM2
KCTD10
CCT2
GRPEL2
ANAPC10
CDC20B
CCT4
DNA2
FCGR1A
CDC26
TGFB1
RGN
NCAPG
FZR1
ATR
SLC11A2
CYTH2
TP53
PIAS1
EEA1
LBP
TRIM28
WDFY1
DDX56
TMEM135
CALCRL
PGK2
BMPR1B
SCARF1
WDFY2
ARFGAP3
MSH2
USF2
SMC1B
HAMP
OBFC1
ENG
SMAD4
HFE2
TBC1D22A
MBL2
ZFYVE16
LRP3
VAMP8
DNAJC13
TFRC
ANAPC2
CCR2
RAB7A
FFAR2
MAF1
MLL4_HUMAN
CHTF18
USP8
ERCC3
PSMD14
ACVRL1
SRSF6
MAP2K7
BLM
CRCP
SMAD2
POLA2
LIG1
CDT1
SLC30A4
TSC1
SLC22A15
PIF1
MAT1A
RPA4
SLC2A13
RNF20
FBXW5
CSTF3
ATP5B
BOD1L1
DDB1
PSMC4
ACVR1
ANAPC11
VBP1
TOP2A
ERCC1
TOP3A
DLG1
RPL23A
POLD4
SNX1
TSC2
LRP1B
GPI
MAD2L1
SKOR1
MALSU1
VPS33B
SRSF4
RAP1A
RIT1
TLR3
SYNJ1
F2RL2
HDAC1
SETBP1
ERCC4
SLC2A7
SMURF2
DVL1
TTI2
BRCA1
ADORA1
UBE2N
CDC27
XPC
SLC2A10
TFR2
BMPR1A
COG4
EXO1
ANAPC4
AP1G1
SIRT1
RAD23B
GADD45G
ACTL8
ATP5A1
TLR1
AHCTF1
GALK2
IPO4
MTOR
ARFGAP2
PCNA
TCF3
C9orf85
CPSF6
CCT3
NSF
MAPRE2
SLC2A2
ZRANB3
OTC
ACVR2A
MSH6
SLC2A1
FANCM
PLK1
CDC20
CHRDL1
CORO1C
TOP2B
RAD52
LRP2
LPL
PAPD7
CCT8L2
NCAPG2
HLTF
SLC2A14
RFC2
SSBP1
SKI
UBE2D1
NEIL1
CLTC
PLAU
CLPB
GNB2L1
ZBED6
MAT2A
SHMT2
ATP6V0A2
SKP2
MAPRE3
PMS1
ATP6V1B1
CLTCL1
DLG3
MUTYH
XPNPEP3
ANAPC1
RUVBL1
ATP5C1
TADA2B
BUB1B
SVOPL
SERPINE1
HGS
ACTR2
CAD
TCP1
PNN
APEX1
MAP2K3
ALDH18A1
SLC2A5
PIGM
ITSN1
RPL9
MDH2
DLST
MLH3
JUN
MXD3
ADORA2A
SMAD3
GRPEL1
KPNB1
CYTH1
AP1S1
MRC1
RPLP0
GDF9
MSH4
CKS2
FSTL1
APC
GAPDH
VPS35
ERBB2IP
NCAPD2
PGM5
MRPS33
ISPD
GALK1
ING1
RAMP2
AADAT
SMAD9
PSMC1
UBE2D3
PMS2
PRM1
SHMT1
NCAPH2
IFNG
FH
ANAPC5
FANCD2
RPA3
HOXA13
GREM1
KIAA0101
GZMA
EIF4EBP1
AHSA2
AMPH
SMARCA5
STK11
N4BP2
PSMD1
TOR1A
BMPER
TPR
ANAPC13
BUB3
CDC23
SMC2
SLC2A9
VEGFA
CTSB
RAB5A
BAMBI
DTL
APEX2
PDS5B
ADM
POLD1
WDR76
CKS1B
CRP
SMURF1
SFTPD
SMC4
SMC1A
ISG15
RABEPK
UBE2S
DLD
XPA
PRUNE
SNIP1
MECP2
UQCRC1
BAZ1B
MBD4
M6PR
RFC5
RPS20
BMP6
E2F1
PRKG1
DMC1
SNX2
EGFR
CX3CL1
ATP6V0D2
ZNF207
RAMP3
BMPR2
MLL
CDC16
NPM1
ERCC5
CCT7
NBL1
CDKN1A
SHPRH
SLC2A12
PHF5A
MCL1
EXOC7
AHDC1
DCAF11
RPL12
CER1
TPT1
DERL1
SMAD6
ATP6V0D1
ANAPC7
UBE2E1
RPA1
PICALM
FCN2
TLR4
RFC3
PSMC5
EPRS
DGKQ
RAB34
BAX
PI4KB
NOG
BMP2
ZBED4
SLC19A1
PDHB
SLC2A11
NTHL1
SLC2A8
RUVBL2
SLC2A3
SLC2A6
TRAP1
NCAPH
CBS
PAPD5
CDKN2A
HMGA2
POLR1C
LIG3
SNX3
PRKDC
SMAD1
USF1
FBXO22
PPTC7
ARHGEF3
MDM2
AHSA1
FOSB
TF
WRNIP1
STAB1
COPS5
POU5F1
ATP6V1B2
MYC
PMPCB
SNX4
MLH1
ZNF524
NDC80
HSPD1
UNG
MSH3
SMAD7
SMC3
CD14
NET1
MGP
CALR3
NRP1
ORC2
CFHR4
279594
ACVR2B
MCPH1
MAPK3
GEN1
CCT8
FEN1
PATZ1
POR
DNAJC7
CDK4
PRC1
SMAD5
ISOC1
RFC4
TBC1D22B