Methotrexate_HepG2/C3A Gene Set

Dataset Tahoe Therapeutics Tahoe 100M Perturbation Atlas
Category transcriptomics
Type cell type
Description Methotrexate perturbation in HepG2/C3A cell line (Tahoe Therapeutics)
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Genes

200 genes differentially expressed following the Methotrexate_HepG2/C3A drug perturbation from the Tahoe Therapeutics Tahoe 100M Perturbation Atlas dataset.

increased expression

Symbol Name Standardized Value
SERPINE1 serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 0.281023
C3 complement component 3 0.27792
DSPP dentin sialophosphoprotein 0.160058
FN1 fibronectin 1 0.155043
TF transferrin 0.154324
ENO1 enolase 1, (alpha) 0.140845
ERRFI1 ERBB receptor feedback inhibitor 1 0.108716
SCD stearoyl-CoA desaturase (delta-9-desaturase) 0.106394
PCBP2 poly(rC) binding protein 2 0.101988
HSP90AB1 heat shock protein 90kDa alpha (cytosolic), class B member 1 0.07482
PEG3 paternally expressed 3 0.0739628
SPTBN1 spectrin, beta, non-erythrocytic 1 0.0728809
AKAP12 A kinase (PRKA) anchor protein 12 0.062864
EML4 echinoderm microtubule associated protein like 4 0.0620953
CP ceruloplasmin (ferroxidase) 0.0618379
RNASET2 ribonuclease T2 0.0604186
TRIO trio Rho guanine nucleotide exchange factor 0.060338
P4HA1 prolyl 4-hydroxylase, alpha polypeptide I 0.05776
HSP90AA1 heat shock protein 90kDa alpha (cytosolic), class A member 1 0.0560123
RERE arginine-glutamic acid dipeptide (RE) repeats 0.0552373
AFDN afadin, adherens junction formation factor 0.0546962
GPAM glycerol-3-phosphate acyltransferase, mitochondrial 0.054553
FNDC3B fibronectin type III domain containing 3B 0.0544341
MYH9 myosin, heavy chain 9, non-muscle 0.0500258
STAT1 signal transducer and activator of transcription 1, 91kDa 0.0490341
RALGAPA2 Ral GTPase activating protein, alpha subunit 2 (catalytic) 0.0480433
SERPINA3 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 0.0468051
ACSL4 acyl-CoA synthetase long-chain family member 4 0.0464775
MAP4K4 mitogen-activated protein kinase kinase kinase kinase 4 0.046465
INSIG2 insulin induced gene 2 0.0459785
HSPD1 heat shock 60kDa protein 1 (chaperonin) 0.045327
KDM3A lysine (K)-specific demethylase 3A 0.044074
RPS18 ribosomal protein S18 0.0434213
DLC1 DLC1 Rho GTPase activating protein 0.0419684
IGF2BP2 insulin-like growth factor 2 mRNA binding protein 2 0.0412894
AMBP alpha-1-microglobulin/bikunin precursor 0.0412723
PTTG1IP pituitary tumor-transforming 1 interacting protein 0.0401683
LRRTM4 leucine rich repeat transmembrane neuronal 4 0.0399896
RNF213 ring finger protein 213 0.0390444
APOB apolipoprotein B 0.0382963
SORL1 sortilin-related receptor, L(DLR class) A repeats containing 0.0378323
ACSL3 acyl-CoA synthetase long-chain family member 3 0.0369729
EIF3A eukaryotic translation initiation factor 3, subunit A 0.0369653
CPE carboxypeptidase E 0.0369294
MSI2 musashi RNA-binding protein 2 0.0366971
NPAS2 neuronal PAS domain protein 2 0.036388
GPC3 glypican 3 0.0363802
RPL3 ribosomal protein L3 0.0360768
CD46 CD46 molecule, complement regulatory protein 0.035543
PGK1 phosphoglycerate kinase 1 0.0353749
HSP90B1 heat shock protein 90kDa beta (Grp94), member 1 0.0342426
CSDE1 cold shock domain containing E1, RNA-binding 0.0342186
RIGI RNA sensor RIG-I 0.0338729
IGF1R insulin-like growth factor 1 receptor 0.033821
PTPRF protein tyrosine phosphatase, receptor type, F 0.0330274
ATP1B1 ATPase, Na+/K+ transporting, beta 1 polypeptide 0.0319138
TGFBI transforming growth factor, beta-induced, 68kDa 0.0316189
EIF2AK2 eukaryotic translation initiation factor 2-alpha kinase 2 0.0312733
MAN1A1 mannosidase, alpha, class 1A, member 1 0.0309709
NFE2L1 nuclear factor, erythroid 2-like 1 0.0308261
HIF1A hypoxia inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) 0.0308147
DDIT4 DNA-damage-inducible transcript 4 0.0300318
TM4SF1 transmembrane 4 L six family member 1 0.0297843
RB1CC1 RB1-inducible coiled-coil 1 0.0294302
PAPOLA poly(A) polymerase alpha 0.0293216
PICALM phosphatidylinositol binding clathrin assembly protein 0.0292867
KTN1 kinectin 1 (kinesin receptor) 0.0290178
ATRN attractin 0.0290037
MX2 MX dynamin-like GTPase 2 0.0282134
ICAM1 intercellular adhesion molecule 1 0.0280759
ATP1A4 ATPase, Na+/K+ transporting, alpha 4 polypeptide 0.0278298
LYZ lysozyme 0.0277158
SESTD1 SEC14 and spectrin domains 1 0.0274279
RUNX1 runt-related transcription factor 1 0.0272589
SLC2A3 solute carrier family 2 (facilitated glucose transporter), member 3 0.0270639
CTNNB1 catenin (cadherin-associated protein), beta 1, 88kDa 0.0267591
PLA2G2A phospholipase A2, group IIA (platelets, synovial fluid) 0.0266676
IFI6 interferon, alpha-inducible protein 6 0.0263338
CAPZB capping protein (actin filament) muscle Z-line, beta 0.0262131
TMEM181 transmembrane protein 181 0.0259852
DSCAM Down syndrome cell adhesion molecule 0.0258873
KMT2C lysine (K)-specific methyltransferase 2C 0.0257021
DHFR dihydrofolate reductase 0.0255471
PTMA prothymosin, alpha 0.0254227
SCAF11 SR-related CTD-associated factor 11 0.0252306
LDHA lactate dehydrogenase A 0.0252054
HLF hepatic leukemia factor 0.0251707
SCN9A sodium channel, voltage gated, type IX alpha subunit 0.0248932
DNAJC5 DnaJ (Hsp40) homolog, subfamily C, member 5 0.0248363
CALR calreticulin 0.0242738
APP amyloid beta (A4) precursor protein 0.0241625
APOE apolipoprotein E 0.0239593
WDFY2 WD repeat and FYVE domain containing 2 0.0238625
VPS54 vacuolar protein sorting 54 homolog (S. cerevisiae) 0.0235887
DDX3Y DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked 0.0232133
EIF4B eukaryotic translation initiation factor 4B 0.0230246
ITPR2 inositol 1,4,5-trisphosphate receptor, type 2 0.0229055
UBC ubiquitin C 0.0227088
HNRNPA2B1 heterogeneous nuclear ribonucleoprotein A2/B1 0.0226951
YES1 YES proto-oncogene 1, Src family tyrosine kinase 0.022488

decreased expression

Symbol Name Standardized Value
MT2A metallothionein 2A -0.21193
IGF2 insulin-like growth factor 2 -0.151313
IGFBP1 insulin-like growth factor binding protein 1 -0.145621
GAPDH glyceraldehyde-3-phosphate dehydrogenase -0.121686
SERPINA1 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 -0.115453
RPS6 ribosomal protein S6 -0.0872024
RPLP1 ribosomal protein, large, P1 -0.0804459
RPLP2 ribosomal protein, large, P2 -0.0536865
SLC38A2 solute carrier family 38, member 2 -0.0524504
RPS8 ribosomal protein S8 -0.0524028
PLCB1 phospholipase C, beta 1 (phosphoinositide-specific) -0.051958
FTL ferritin, light polypeptide -0.0482413
RPL37A ribosomal protein L37a -0.0470394
SVIL supervillin -0.0468297
RPS24 ribosomal protein S24 -0.0460674
RPL11 ribosomal protein L11 -0.0424862
RPL35A ribosomal protein L35a -0.04211
RPS23 ribosomal protein S23 -0.0420289
RPL34 ribosomal protein L34 -0.0412096
RPS19 ribosomal protein S19 -0.0408989
JMJD1C jumonji domain containing 1C -0.0404105
RPS12 ribosomal protein S12 -0.0382348
DHRS2 dehydrogenase/reductase (SDR family) member 2 -0.0369939
GOLGB1 golgin B1 -0.0355753
RPL19 ribosomal protein L19 -0.0354019
RPS16 ribosomal protein S16 -0.0349447
RPL26 ribosomal protein L26 -0.0347325
GBE1 glucan (1,4-alpha-), branching enzyme 1 -0.0346396
FAM107B family with sequence similarity 107, member B -0.0344908
CCL20 chemokine (C-C motif) ligand 20 -0.0341909
RPS10 ribosomal protein S10 -0.0340754
TIMP1 TIMP metallopeptidase inhibitor 1 -0.0337742
RPL5 ribosomal protein L5 -0.0330387
EPAS1 endothelial PAS domain protein 1 -0.0327371
ITGA2 integrin, alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) -0.0325346
CRY1 cryptochrome circadian clock 1 -0.0323569
ACTG1 actin gamma 1 -0.0313072
IER3 immediate early response 3 -0.0312702
RPL17-C18ORF32 RPL17-C18orf32 readthrough -0.0304074
SNTB1 syntrophin, beta 1 (dystrophin-associated protein A1, 59kDa, basic component 1) -0.0299513
RPL28 ribosomal protein L28 -0.0299074
RPS20 ribosomal protein S20 -0.0295721
RPL7A ribosomal protein L7a -0.0295539
TNFSF14 tumor necrosis factor (ligand) superfamily, member 14 -0.0294943
RPL23 ribosomal protein L23 -0.0294441
RPS25 ribosomal protein S25 -0.0294185
PDLIM5 PDZ and LIM domain 5 -0.0291559
AGAP1 ArfGAP with GTPase domain, ankyrin repeat and PH domain 1 -0.0287044
ERN1 endoplasmic reticulum to nucleus signaling 1 -0.0284017
RPS15 ribosomal protein S15 -0.0279679
RPL38 ribosomal protein L38 -0.0270813
LOC112694756 uncharaterized LOC112694756 -0.0269001
CPEB4 cytoplasmic polyadenylation element binding protein 4 -0.0267069
RPL10A ribosomal protein L10a -0.0267061
CRIM1 cysteine rich transmembrane BMP regulator 1 (chordin-like) -0.0264897
JAG1 jagged 1 -0.0259962
TPT1 tumor protein, translationally-controlled 1 -0.0254781
TM9SF3 transmembrane 9 superfamily member 3 -0.025399
RPL30 ribosomal protein L30 -0.0249806
ANXA5 annexin A5 -0.0249732
MAP1LC3B microtubule-associated protein 1 light chain 3 beta -0.0247431
CCDC88A coiled-coil domain containing 88A -0.0236724
MALRD1 MAM and LDL receptor class A domain containing 1 -0.0236054
PRAG1 PEAK1 related, kinase-activating pseudokinase 1 -0.0234811
HM13 histocompatibility (minor) 13 -0.0233071
RPLP0 ribosomal protein, large, P0 -0.0231891
RAB1A RAB1A, member RAS oncogene family -0.0231704
STK17A serine/threonine kinase 17a -0.0230348
APOA2 apolipoprotein A-II -0.0229912
RPS27A ribosomal protein S27a -0.0229387
HIVEP2 human immunodeficiency virus type I enhancer binding protein 2 -0.0228005
RPL9 ribosomal protein L9 -0.0227118
RPL12 ribosomal protein L12 -0.02271
RPS21 ribosomal protein S21 -0.0225729
LCOR ligand dependent nuclear receptor corepressor -0.0223743
CSGALNACT2 chondroitin sulfate N-acetylgalactosaminyltransferase 2 -0.0218023
RAB22A RAB22A, member RAS oncogene family -0.0217759
RPL36A ribosomal protein L36a -0.0213152
RPL4 ribosomal protein L4 -0.0212157
ID1 inhibitor of DNA binding 1, dominant negative helix-loop-helix protein -0.0211737
RPS17 ribosomal protein S17 -0.0209669
RPL32 ribosomal protein L32 -0.0209376
TSC22D2 TSC22 domain family, member 2 -0.0208625
ZNF451 zinc finger protein 451 -0.0208185
YAP1 Yes-associated protein 1 -0.0207268
ATF6 activating transcription factor 6 -0.0206773
USP15 ubiquitin specific peptidase 15 -0.0206191
N4BP2L2 NEDD4 binding protein 2-like 2 -0.0205357
EXOC6B exocyst complex component 6B -0.0205319
PSME4 proteasome (prosome, macropain) activator subunit 4 -0.020504
REV3L REV3-like, polymerase (DNA directed), zeta, catalytic subunit -0.020491
MAP3K2 mitogen-activated protein kinase kinase kinase 2 -0.0203248
SERTAD2 SERTA domain containing 2 -0.0200056
ABTB2 ankyrin repeat and BTB (POZ) domain containing 2 -0.0197197
RACK1 receptor for activated C kinase 1 -0.0195072
AAK1 AP2 associated kinase 1 -0.0194316
NCOA2 nuclear receptor coactivator 2 -0.0193488
RNASEH2A ribonuclease H2, subunit A -0.0191589
RPL7 ribosomal protein L7 -0.0188928
RPS14 ribosomal protein S14 -0.018573