RNAi

Gene Info

  • Species: Human (Homo sapiens)
  • GeneID: 7168
  • Symbol: TPM1
  • Description: tropomyosin 1
DataSource: http://genomernai.dkfz.de/v16/genedetails/7168

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Stable_ID Entrez_ID Gene_ID Gene_Symbol Reagent_ID Score Phenotype Conditions Follow_Up Comment Screen_Title Publication_Title Authors Publication_Year Pubmed_ID Biosource Biomodel Assay Method Library Scope Reagent_Type Score_Type Cutoff Notes
GR00053-A 7168 NM_000366 TPM1 np sp Increased gamma-H2AX phosphorylation no group 2 Genome stability A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. Paulsen et al. 2009 19647519 Cell line HeLa gamma-H2AX phosphorylation and DNA content Fluorescence siARRAY human genome siRNA library Genome-wide siRNA p-value Complex criteria Confidence groupings from 4 to 1 (highest level of confidence in group 4)
GR00054-A 7168 NM_000366 TPM1 np 0.749 none no Combinatorial effect with paclitaxel Synthetic lethal screen identification of chemosensitizer loci in cancer cells. Whitehurst et al. 2007 17429401 Cell line NCI-H1155 Viability (synthetic lethal) ATP level # G-005000-01 Genome-wide siRNA Paclitaxel/control ratio Complex criteria Additional information about 87 high-confidence hits
7168 7168 TPM1 np np Decreased viability yes deconvoluted validated siRNAs: 2/2
GR00055-A-2 7168 7168 TPM1 np np Decreased viability yes Epithelial cell migration (2) Identification of genes that regulate epithelial cell migration using an siRNA screening approach. Simpson et al. 2008 19160483 Cell line MCF-10A overexpressing BCL2 Cell migration and viability Microscopy and fluorescence SMARTpool siRNA library Selected genes siRNA Area score and Alamar score Complex criteria
GR00055-A-3 7168 7168 TPM1 np np Decreased viability no Epithelial cell migration (3) Identification of genes that regulate epithelial cell migration using an siRNA screening approach. Simpson et al. 2008 19160483 Cell line MCF-10A overexpressing ERBB2 Cell migration and viability Microscopy and fluorescence SMARTpool siRNA library and MAR library Selected genes siRNA Area score and Alamar score Complex criteria
GR00056-A 7168 NM_000366 TPM1 np 1.134 none no Melanogenesis Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells. Ganesan et al. 2008 19057677 Cell line MNT-1 Melanin protein expression and viability Absorbance and luminescence rp Genome-wide siRNA Normalized absorbance ratio > 2 standard deviations below mean Additional information about a secondary screen (retest to determine false-positive rate)
GR00057-A-1 7168 NM_000366 TPM1 M-017837-00 2.58 none no Wnt/beta-catenin pathway regulation (1) A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. Tang et al. 2008 18621708 Cell line HeLa Wnt pathway reporter Luminescence Human siArray siRNA library Genome-wide siRNA Z-score > 4 Screen without Wnt3A stimulation. Additional information about secondary screens (Dharmacon and Qiagen libraries).
GR00057-A-2 7168 NM_000366 TPM1 M-017837-00 sp none no Wnt/beta-catenin pathway regulation (2) A genome-wide RNAi screen for Wnt/beta-catenin pathway components identifies unexpected roles for TCF transcription factors in cancer. Tang et al. 2008 18621708 Cell line HeLa Wnt pathway reporter Luminescence Human siArray siRNA library Genome-wide siRNA Complex, SP Complex criteria Screen with Wnt3A stimulation. Additional information about secondary screens (Dharmacon and Qiagen libraries).
GR00095-A 7168 NM_000366 TPM1 np np none p53 pathway components A large-scale RNAi screen in human cells identifies new components of the p53 pathway Berns et al. 2004 15042092 Cell line BJ-TERT-tsLT fibroblasts Proliferation Colony-forming cell assay Nki library Genome-wide shRNA np np
GR00098-A-1 7168 ENSG00000140416 TPM1 ENSG00000140416 sp none no Cell division (1) Genome-scale RNAi profiling of cell division in human tissue culture cells. Kittler et al. 2007 17994010 Cell line HeLa Cell number and DNA content Laser scanning cytometry rp Genome-wide esiRNA Complex, sp Complex criteria
GR00123-A 7168 NM_000366 TPM1 142071, 142072, 142073, 141673, 141672, 141671 np none Combinatorial effect with nutlin-3 An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors Brummelkamp et al. 2006 16474381 Cell line MCF-7 Viability Fluoresence Nki library Genome-wide shRNA log2 ratio np
GR00133-A-1 7168 7168 TPM1 np -0.026715 none no Salmonella enterica subspecies 1 serovar Typhimurium invasion (1) RNAi screen of Salmonella invasion shows role of COPI in membrane targeting of cholesterol and Cdc42. Misselwitz et al. 2011 21407211 Cell line HeLa Gentamycin protection invasion assay Fluorescence Druggable genome library V2.0 Druggable genes siRNA log2 median Complex criteria
GR00149-A-1 7168 7168 TPM1 8429 20.31 none no Ciliogenesis and cilium length (1) Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al. 2010 20393563 Cell line htRPE Smoothed protein expression Fluorescence Human druggable genome siRNA library V3.1 Druggable genes siRNA Normalized percent inhibition > 1.5 OR < -1.5 standard deviations from mean
GR00149-A-1 7168 7168 TPM1 8429 52.97 none no Ciliogenesis and cilium length (1) Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al. 2010 20393563 Cell line htRPE Smoothed protein expression Fluorescence Human druggable genome siRNA library V3.1 Druggable genes siRNA Normalized percent inhibition > 1.5 OR < -1.5 standard deviations from mean
GR00149-A-1 7168 7168 TPM1 8523 -12.75 none no Ciliogenesis and cilium length (1) Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al. 2010 20393563 Cell line htRPE Smoothed protein expression Fluorescence Human druggable genome siRNA library V3.1 Druggable genes siRNA Normalized percent inhibition > 1.5 OR < -1.5 standard deviations from mean
GR00149-A-1 7168 7168 TPM1 8523 10.1 none no Ciliogenesis and cilium length (1) Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al. 2010 20393563 Cell line htRPE Smoothed protein expression Fluorescence Human druggable genome siRNA library V3.1 Druggable genes siRNA Normalized percent inhibition > 1.5 OR < -1.5 standard deviations from mean
GR00149-A-1 7168 7168 TPM1 118352 21.17 none no Ciliogenesis and cilium length (1) Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al. 2010 20393563 Cell line htRPE Smoothed protein expression Fluorescence Human druggable genome siRNA library V3.1 Druggable genes siRNA Normalized percent inhibition > 1.5 OR < -1.5 standard deviations from mean
GR00149-A-1 7168 7168 TPM1 118352 28.52 none no Ciliogenesis and cilium length (1) Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al. 2010 20393563 Cell line htRPE Smoothed protein expression Fluorescence Human druggable genome siRNA library V3.1 Druggable genes siRNA Normalized percent inhibition > 1.5 OR < -1.5 standard deviations from mean
GR00149-A-1 7168 7168 TPM1 118353 24.42 none no Ciliogenesis and cilium length (1) Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al. 2010 20393563 Cell line htRPE Smoothed protein expression Fluorescence Human druggable genome siRNA library V3.1 Druggable genes siRNA Normalized percent inhibition > 1.5 OR < -1.5 standard deviations from mean
GR00149-A-1 7168 7168 TPM1 118353 -18.74 none no Ciliogenesis and cilium length (1) Functional genomic screen for modulators of ciliogenesis and cilium length. Kim et al. 2010 20393563 Cell line htRPE Smoothed protein expression Fluorescence Human druggable genome siRNA library V3.1 Druggable genes siRNA Normalized percent inhibition > 1.5 OR < -1.5 standard deviations from mean
GR00151-A-1 7168 ENSG00000140416 TPM1 np 0.53 none no Homologous recombination DNA double-strand break repair (HR-DSBR) (1) A genome-scale DNA repair RNAi screen identifies SPG48 as a novel gene associated with hereditary spastic paraplegia. SÅ‚abicki et al. 2010 20613862 Cell line HeLa (HR-DSBR) DR-GFP reporter Flow cytometry Custom-made Genome-wide esiRNA Z-score < -2 OR > 2
GR00180-A-1 7168 7168 TPM1 PL-50019 0.928 none no Hepatitis C virus replication (1) A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Tai et al. 2009 19286138 Cell line Huh7/Rep-Feo HCV replicon RNA copy number Luminescence siARRAY Human Genome siRNA Library Genome-wide siRNA q-value Complex criteria
GR00181-A 7168 NM_000366 TPM1 np -71.76695064 Synthetic lethal with imatinib mesylate no at least 2 unique shRNAs identified Combinatorial effect with imatinib Wnt/Ca2+/NFAT signaling maintains survival of Ph+ leukemia cells upon inhibition of Bcr-Abl. Gregory et al. 2010 20609354 Cell line K562 Viability (synthetic lethal) PCR and Affymetrix microarray GeneNet lentiviral human 50K shRNA library Random genes shRNA Fold change Complex criteria
GR00181-A 7168 NM_001018008 TPM1 np -8.949035053 Synthetic lethal with imatinib mesylate no at least 2 unique shRNAs identified Combinatorial effect with imatinib Wnt/Ca2+/NFAT signaling maintains survival of Ph+ leukemia cells upon inhibition of Bcr-Abl. Gregory et al. 2010 20609354 Cell line K562 Viability (synthetic lethal) PCR and Affymetrix microarray GeneNet lentiviral human 50K shRNA library Random genes shRNA Fold change Complex criteria
GR00184-A-1 7168 NM_000366 TPM1 M-017837-00 -2.68636767118652 Decreased POU5F1-GFP protein expression yes Self-renewal and pluripotency in human embryonic stem cells (1) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 POU5F1 protein expression Fluorescence SMARTpool siRNA library Genome-wide siRNA Z-score < -2
GR00184-A-2 7168 NM_001018005 TPM1 D-017837-03 0.268567233039371 Decreased OCT4 protein expression yes Self-renewal and pluripotency in human embryonic stem cells (2) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-2 7168 NM_001018005 TPM1 D-017837-04 0.306250120451962 Decreased OCT4 protein expression yes Self-renewal and pluripotency in human embryonic stem cells (2) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-2 7168 NM_001018005 TPM1 D-017837-17 0.381210193756096 Decreased OCT4 protein expression yes Self-renewal and pluripotency in human embryonic stem cells (2) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-2 7168 NM_001018005 TPM1 D-017837-18 0.424535921243048 Decreased OCT4 protein expression yes Self-renewal and pluripotency in human embryonic stem cells (2) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-3 7168 NM_001018005 TPM1 D-017837-18 0.51118812231711 Decreased NANOG protein expression yes Self-renewal and pluripotency in human embryonic stem cells (3) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-3 7168 NM_001018005 TPM1 D-017837-03 0.250424478222902 Decreased NANOG protein expression yes Self-renewal and pluripotency in human embryonic stem cells (3) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-3 7168 NM_001018005 TPM1 D-017837-04 0.311199811816752 Decreased NANOG protein expression yes Self-renewal and pluripotency in human embryonic stem cells (3) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-3 7168 NM_001018005 TPM1 D-017837-17 0.455827144469636 Decreased NANOG protein expression yes Self-renewal and pluripotency in human embryonic stem cells (3) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-4 7168 NM_001018005 TPM1 D-017837-17 0.360693843222268 Decreased POU5F1-GFP protein expression yes Self-renewal and pluripotency in human embryonic stem cells (4) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 POU5F1 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-4 7168 NM_001018005 TPM1 D-017837-18 0.382059977348908 Decreased POU5F1-GFP protein expression yes Self-renewal and pluripotency in human embryonic stem cells (4) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 POU5F1 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-4 7168 NM_001018005 TPM1 D-017837-03 0.215399553472391 Decreased POU5F1-GFP protein expression yes Self-renewal and pluripotency in human embryonic stem cells (4) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 POU5F1 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-4 7168 NM_001018005 TPM1 D-017837-04 0.270772063224193 Decreased POU5F1-GFP protein expression yes Self-renewal and pluripotency in human embryonic stem cells (4) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line hESC H1 POU5F1 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-5 7168 NM_001018005 TPM1 D-017837-03 0.854522728036115 none yes Self-renewal and pluripotency in human embryonic stem cells (5) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES2 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-5 7168 NM_001018005 TPM1 D-017837-17 1.02112346735531 none yes Self-renewal and pluripotency in human embryonic stem cells (5) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES2 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-5 7168 NM_001018005 TPM1 D-017837-18 0.692228490394207 Decreased OCT4 protein expression yes Self-renewal and pluripotency in human embryonic stem cells (5) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES2 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-5 7168 NM_001018005 TPM1 D-017837-04 0.842406243899409 none yes Self-renewal and pluripotency in human embryonic stem cells (5) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES2 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-6 7168 NM_001018005 TPM1 D-017837-03 0.801274699836202 none yes Self-renewal and pluripotency in human embryonic stem cells (6) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES2 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-6 7168 NM_001018005 TPM1 D-017837-04 0.827143323946285 none yes Self-renewal and pluripotency in human embryonic stem cells (6) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES2 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-6 7168 NM_001018005 TPM1 D-017837-18 0.768043296131676 none yes Self-renewal and pluripotency in human embryonic stem cells (6) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES2 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-6 7168 NM_001018005 TPM1 D-017837-17 0.86720415925127 none yes Self-renewal and pluripotency in human embryonic stem cells (6) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES2 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-7 7168 NM_001018005 TPM1 D-017837-04 0.709782029297686 Decreased OCT4 protein expression yes Self-renewal and pluripotency in human embryonic stem cells (7) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES3 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-7 7168 NM_001018005 TPM1 D-017837-18 0.386087340464017 Decreased OCT4 protein expression yes Self-renewal and pluripotency in human embryonic stem cells (7) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES3 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-7 7168 NM_001018005 TPM1 D-017837-03 0.850338003135147 none yes Self-renewal and pluripotency in human embryonic stem cells (7) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES3 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-7 7168 NM_001018005 TPM1 D-017837-17 0.589508886934812 Decreased OCT4 protein expression yes Self-renewal and pluripotency in human embryonic stem cells (7) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES3 OCT4 protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-8 7168 NM_001018005 TPM1 D-017837-18 0.355512292681131 Decreased NANOG protein expression yes Self-renewal and pluripotency in human embryonic stem cells (8) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES3 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-8 7168 NM_001018005 TPM1 D-017837-04 0.675318227554455 Decreased NANOG protein expression yes Self-renewal and pluripotency in human embryonic stem cells (8) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES3 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-8 7168 NM_001018005 TPM1 D-017837-03 0.738871784056463 Decreased NANOG protein expression yes Self-renewal and pluripotency in human embryonic stem cells (8) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES3 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00184-A-8 7168 NM_001018005 TPM1 D-017837-17 0.508234480070805 Decreased NANOG protein expression yes Self-renewal and pluripotency in human embryonic stem cells (8) A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity. Chia et al. 2010 20953172 Cell line HES3 NANOG protein expression Fluorescence siGENOME siRNA library Selected genes siRNA Relative expression < 0.75
GR00196-A-1 7168 ENSG00000140416 np sp none no TP53 interactions (1) A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly. Krastev et al. 2011 21642980 Cell line HCT116 ( wildtype and TP53 knockout) TP53 protein expression and viability Fluorescence rp Genome-wide esiRNA Complex, sp Complex criteria
GR00197-A-1 7168 7168 TPM1 M-017837-00 -0.250629646 none no Human papillomavirus oncogene expression regulation (1) Genome-wide siRNA screen identifies SMCX, EP400, and Brd4 as E2-dependent regulators of human papillomavirus oncogene expression. Smith et al. 2010 20133580 Cell line C33A/BE2/18LCR c4 HPV18 LCR reporter activity Luminescence Human siGENOME SMARTpool library Genome-wide siRNA Z-score > Author-submitted data. Phenotype strength according to Z-scores: weak: 2 - 3; moderate: 3 - 5; strong: > 5
GR00210-A 7168 7168 TPM1 np sp none no Focal adhesion formation Multiparametric analysis of focal adhesion formation by RNAi-mediated gene knockdown. Winograd-Katz et al. 2009 19667130 Cell line HeLa paxillin protein expression Fluorescence SMARTpool siARRAY siRNA Libraries Kinases, phosphatases and selected genes siRNA Z-score > 3.5 OR < -3.5
GR00236-A-1 7168 7168 TPM1 M-017837-00 1.10805397148215 none no Homologous recombination DNA double-strand break repair (HR-DSBR) (1) A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response. Adamson et al. 2012 22344029 Cell line DR-U2OS (HR-DSBR) DR-GFP reporter and DNA content Fluorescence Human siGENOME siRNA (G-005000-05) Genome-wide siRNA Relative HR ratio < ~0.4 OR > 1.88 Cutoff values correspond 2 standard deviations from the screen-wide mean
GR00240-S-1 7168 NM_000366 TPM1 M-017837-00 1.25 none yes TRAIL-induced apoptosis (1) A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. Kranz and Boutros 2014 24442637 Cell line U251MG Viability Luminescence SMART-pool siRNA Genome-wide siRNA Z-score > 4 Author-submitted data
GR00240-S-2 7168 NM_000366 TPM1 M-017837-00 -0.83 none no Z-score 0.5065 TRAIL-induced apoptosis (2) A synthetic lethal screen identifies FAT1 as an antagonist of caspase-8 in extrinsic apoptosis. Kranz and Boutros 2014 24442637 Cell line U251MG Viability (synthetic lethal) Luminescence SMART-pool siRNA Genome-wide siRNA Differential score > 3.6 AND viability Z-score < 4 Author-submitted data. Z-scores from viability screen (1) are considered in score interpretation for this screen.
GR00242-A-1 7168 NM_000366 TPM1 np sp none no Selective autophagy regulation (1) Image-based genome-wide siRNA screen identifies selective autophagy factors. Orvedahl et al. 2011 22020285 Cell line HeLa/GFP-LC3 Sindbis virus (SIN) capsid SIN-mCherry.capsid and autophagosome GFP–LC3 protein expression Fluorescence siGenome Genome-wide siRNA Z-score Complex criteria
GR00247-A-1 7168 TPM1 np sp none rank: 11702 Regulation of FOXO1 nuclear localization (1) Whole genome siRNA cell-based screen links mitochondria to Akt signaling network through uncoupling of electron transport chain. Senapedis et al. 2011 21460183 Cell line U2OS EGFP-FOXO1a protein expression and DNA content Fluorescence Human Genome library Genome-wide siRNA Complex, sp Complex criteria
GR00249-S 7168 7168 TPM1 J-017837-05 -0.45722 none no number of cells compared to control (%): 92.40 Vaccinia virus (VACV) infection Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al. 2013 23401514 Cell line HeLa Vaccinia virus VACV IHD-J/GFP protein expression and DNA content Fluorescence Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus Genome-wide siRNA Z-score > Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.
GR00249-S 7168 7168 TPM1 M-017837-01 -0.51977 Decreased viability no number of cells compared to control (%): 49.51 Vaccinia virus (VACV) infection Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al. 2013 23401514 Cell line HeLa Vaccinia virus VACV IHD-J/GFP protein expression and DNA content Fluorescence Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus Genome-wide siRNA Z-score > Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.
GR00249-S 7168 7168 TPM1 s14340 -0.44814 none no number of cells compared to control (%): 88.49 Vaccinia virus (VACV) infection Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al. 2013 23401514 Cell line HeLa Vaccinia virus VACV IHD-J/GFP protein expression and DNA content Fluorescence Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus Genome-wide siRNA Z-score > Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.
GR00249-S 7168 7168 TPM1 s14341 0.01172 none no number of cells compared to control (%): 99.73 Vaccinia virus (VACV) infection Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al. 2013 23401514 Cell line HeLa Vaccinia virus VACV IHD-J/GFP protein expression and DNA content Fluorescence Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus Genome-wide siRNA Z-score > Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.
GR00249-S 7168 7168 TPM1 s14342 0.44986 none no number of cells compared to control (%): 87.33 Vaccinia virus (VACV) infection Human genome-wide RNAi screen reveals a role for nuclear pore proteins in poxvirus morphogenesis. Sivan et al. 2013 23401514 Cell line HeLa Vaccinia virus VACV IHD-J/GFP protein expression and DNA content Fluorescence Silencer Select Version 4, siGENOME SMARTpool and OnTargetPlus Genome-wide siRNA Z-score > Author-submitted data. Primary screen. Decreased viability phenotype if number of cells compared to control < 50 %.
GR00253-A 7168 NM_000366 TPM1 np -0.778 none hepcidin regulation Unbiased RNAi screen for hepcidin regulators links hepcidin suppression to proliferative Ras/RAF and nutrient-dependent mTOR signaling. Mleczko-Sanecka et al. 2014 24385536 Cell line Huh7 hepcidin::fluc mRNA expression Luminescence siGenome siARRAY SMARTpool Genome-wide siRNA Z-score > Cutoff <
GR00255-A-1 7168 7168 TPM1 TRCN0000062148, TRCN0000062149, TRCN0000062150, TRCN0000062151, TRCN0000062152 -0.122937871 none Negative genetic interactions (1) A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al. 2013 24104479 Cell line HCT116 shRNA abundance Microarray np Genome-wide shRNA differential Gene Activity Ranking Profile (dGARP) < -1.0 HCT116 BLM-/- and HCT116 BLM+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)
GR00255-A-2 7168 7168 TPM1 TRCN0000062148, TRCN0000062149, TRCN0000062150, TRCN0000062151, TRCN0000062152 -0.230488369 none Negative genetic interactions (2) A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al. 2013 24104479 Cell line HCT116 shRNA abundance Microarray np Genome-wide shRNA differential Gene Activity Ranking Profile (dGARP) < -1.0 HCT116 MUS81-/- and HCT116 MUS81+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)
GR00255-A-3 7168 7168 TPM1 TRCN0000062148, TRCN0000062149, TRCN0000062150, TRCN0000062151, TRCN0000062152 -0.208253083 none Negative genetic interactions (3) A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al. 2013 24104479 Cell line HCT116 shRNA abundance Microarray np Genome-wide shRNA differential Gene Activity Ranking Profile (dGARP) < -1.2 HCT116 PTEN-/- and HCT116 PTEN+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)
GR00255-A-4 7168 7168 TPM1 TRCN0000062148, TRCN0000062149, TRCN0000062150, TRCN0000062151, TRCN0000062152 0.218825422 none Negative genetic interactions (4) A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al. 2013 24104479 Cell line HCT116 shRNA abundance Microarray np Genome-wide shRNA differential Gene Activity Ranking Profile (dGARP) < -1.2 HCT116 PTTG1-/- and HCT116 PTTG1+/+ cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)
GR00255-A-5 7168 7168 TPM1 TRCN0000062148, TRCN0000062149, TRCN0000062150, TRCN0000062151, TRCN0000062152 -0.020225655 none Negative genetic interactions (5) A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar et al. 2013 24104479 Cell line HCT116 shRNA abundance Microarray np Genome-wide shRNA differential Gene Activity Ranking Profile (dGARP) < -0.8 HCT116 KRASG13D/- and HCT116 KRAS+/- cells used. Cutoff corresponds to p-value < 0.05. Additional information about a secondary screen (genetic interactions with Cetuximab/Erbitux in LIM1215 cells)
GR00293-A 7168 TPM1 np 0.708 none Combinatorial effect with paclitaxel Mechanisms Promoting Escape from Mitotic Stress−Induced Tumor Cell Death Sinnott et al. 2014 24860162 Cell line HCC366 Viability Luminescence Thermo-Fisher Genome-wide siRNA Z-score < -2.5 Final hits according to the author are indicated in the comment.
GR00300-A 7168 TPM1 TRCN0000062150, TRCN0000062152, TRCN0000062151, TRCN0000062148, TRCN0000062149 0 none Combinatorial effect with RAF inhibitor PLX4720 A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. Whittaker et al. 2013 23288408 Cell line A375 shRNA abundance Sequencing TRC Genome-wide shRNA Number of shRNAs ranked Top1000 > 2 The A375 cell line used here harbours the BRAF V600E mutation and is therefore sensitive to RAF inhibitors.
GR00303-A 7168 NM_000366 TPM1 np -1.75 none Clear cell renal cell carcinoma (ccRCC) survival regulation Genome-wide RNA interference analysis of renal carcinoma survival regulators identifies MCT4 as a Warburg effect metabolic target Gerlinger et al. 2012 22362593 Cell line VHL-deficient RCC4 Proliferation and Viability Fluorescence np Genome-wide siRNA Z-score < In the phenotype data duplicates were in the original document, which have been removed.
GR00310-A-1 7168 7168 TPM1 np -0.7 none Sindbis virus (SINV) infection (1) Genome-Wide RNAi Screen Identifies Novel Host Proteins Required for Alphavirus Entry Ooi et al. 2013 24367265 Cell line U2OS Sindbis virus (SINV) reporter Luminescence Ambion Silencer V3 Genome-wide siRNA Z-score < -3 OR > 2
7168 7168 TPM1 np 54.6 none 61,9% viability
GR00313-A 7168 NM_000366, NM_001018004, NM_001018005, NM_001018006, NM_001018007, NM_001018008, NM_001018020 TPM1 np -0.2 none TNF-alpha pathway regulation A Genome-Wide RNA Interference Screen Identifies Caspase 4 as a Factor Required for Tumor Necrosis Factor Alpha Signaling. Nickles et al. 2012 22733992 Cell line HEK293T NFkappaB pathway reporter Luminescence Qiagen Genome-wide siRNA Z-score < Additional filters were a reduction in firefly luciferase levels by at least 50% compared to the mean of the experiment and a concomitant reduction of renilla luciferase expression of not more than 30%.
GR00318-A 7168 7168 TPM1 np 0.939 none siRNA set: druggable genome Huntingtin toxicity A Genome-Scale RNA–Interference Screen Identifies RRAS Signaling as a Pathologic Feature of Huntington’s Disease Miller et al. 2012 23209424 Cell line HEK293T Caspase 3/7 activity Fluorescence Dharmacon Selected genes siRNA Sum of normalized caspase 3/7 activity mean and standard error < 0.683 HEK293T cells were cotransfected with mutant Huntingtin fused to GFP (Htt1-558141Q-GFP).
GR00327-A 7168 1228 TLR8 CLL-H-025677 1.430018291708183 none Tumor formation An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation Wolf et al. 2013 24292671 Cell line SUM-149 shRNA abundance Next-generation sequencing Decipher library module 1 Selected genes shRNA Z-score > 2.24 Genes were scored as hit if at least 2 shRNAs scored as hit, see comment.
GR00327-A 7168 1228 TLR8 CLL-H-025680 -0.5743866496653479 none Tumor formation An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation Wolf et al. 2013 24292671 Cell line SUM-149 shRNA abundance Next-generation sequencing Decipher library module 1 Selected genes shRNA Z-score > 2.24 Genes were scored as hit if at least 2 shRNAs scored as hit, see comment.
GR00327-A 7168 1228 TLR8 CLL-H-025679 0.8801609403848082 none Tumor formation An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation Wolf et al. 2013 24292671 Cell line SUM-149 shRNA abundance Next-generation sequencing Decipher library module 1 Selected genes shRNA Z-score > 2.24 Genes were scored as hit if at least 2 shRNAs scored as hit, see comment.
GR00327-A 7168 1228 TLR8 CLL-H-025678 -0.9422988413433027 none Tumor formation An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation Wolf et al. 2013 24292671 Cell line SUM-149 shRNA abundance Next-generation sequencing Decipher library module 1 Selected genes shRNA Z-score > 2.24 Genes were scored as hit if at least 2 shRNAs scored as hit, see comment.
GR00327-A 7168 1228 TLR8 CLL-H-025681 1.2987859592544002 none Tumor formation An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation Wolf et al. 2013 24292671 Cell line SUM-149 shRNA abundance Next-generation sequencing Decipher library module 1 Selected genes shRNA Z-score > 2.24 Genes were scored as hit if at least 2 shRNAs scored as hit, see comment.
GR00327-A 7168 1228 TLR8 CLL-H-025676 -0.1391752482139422 none Tumor formation An in vivo RNAi screen identifies SALL1 as a tumor suppressor in human breast cancer with a role in CDH1 regulation Wolf et al. 2013 24292671 Cell line SUM-149 shRNA abundance Next-generation sequencing Decipher library module 1 Selected genes shRNA Z-score > 2.24 Genes were scored as hit if at least 2 shRNAs scored as hit, see comment.
7168 7168 TPM1 -0.009999999999999981 none
GR00376-A-1 7168 7168 TPM1 0.012440028 none Mitigators of SS1P-induced immunotoxicity Whole-genome RNAi screen highlights components of the endoplasmic reticulum/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity Pasetto et al. 2015 25713356 Cell line KB cells Viability Luminescence Ambion Silencer Select Version 4 Genome-wide siRNA RSA P-value <0.001 SS1P was applied in a "high dose", ≈EC90, 13 ng/ml. Cutoff was derived from data submitted to Pubchem (ID 1117281). Reagent sequences but no ID
GR00376-A-2 7168 7168 TPM1 0.772638493 none Sensitizers of SS1P-induced immunotoxicity Whole-genome RNAi screen highlights components of the endoplasmic reticulum/Golgi as a source of resistance to immunotoxin-mediated cytotoxicity Pasetto et al. 2015 25713356 Cell line KB cells Viability Luminescence Ambion Silencer Select Version 4 Genome-wide siRNA RSA P-value <0.001 SS1P was applied in a "low dose", ≈EC30, 3 ng/ml. Cutoff was derived from data submitted to PubChem (ID 1117281). Reagent sequences but no ID
GR00378-A 7168 TPM1 -1.881427619 none Poliovirus vaccine production Engineering Enhanced Vaccine Cell Lines To Eradicate Vaccine-Preventable Diseases: the Polio End Game van der Sanden et al. 2015 26581994 Cell line HEp-2C Infection with Attenuated Poliovirus ELISA Dharmacon Genome-wide siRNA Z-score > For infection, a single lot of the attenuated Sabin type 2 poliovirus was used for the screen. Gene IDs were not provided, only the gene name/symbol
7168 NM_000366 TPM1 70.199 none
GR00386-A-1 7168 7168 TPM1 52.6027478176241 Decreased viability NOD2 stimulation by MDP A genome-wide small interfering RNA (siRNA) screen reveals nuclear factor-κB (NF-κB)-independent regulators of NOD2-induced interleukin-8 (IL-8) secretion. Warner et al. 2014 25170077 Cell line HEK293 stably expressing NOD2 Viability Luminescence Dharmacon Genome-wide siRNA Percentage growth Decreased: <70, increased: >120 Reagent IDs not provided
GR00386-A-2 7168 7168 TPM1 -307.3 Increased IL-8 secretion MDP-induced IL-8 secretion A genome-wide small interfering RNA (siRNA) screen reveals nuclear factor-κB (NF-κB)-independent regulators of NOD2-induced interleukin-8 (IL-8) secretion. Warner et al. 2014 25170077 Cell line HEK293 stably expressing NOD2 IL-8 secretion ELISA Dharmacon Genome-wide siRNA Percent inhibition of IL-8 secretion Increased: <-300, Decreased: >60 Concentration of IL-8 was measured from cell supernatants by sandwich ELISA. IL-8 values (pg/ml) were normalized to IL-8 secreted in cells treated with RIPK2-specific siRNA (100% inhibition) and non-targeting siRNA (0% inhibition). Secondary validating screen assessed 554 genes whose silencing affected MDP-induced IL-8 secretion in the primary screen. Final validated IL-8 regulators (positive or negative) are listed in the comments column. Reagent IDs not provided