Genotoxicity pathway (Homo sapiens)

From WikiPathways

Jump to: navigation, search
116, 13, 165, 192, 5, 1951752, 3, 5, 16, 17, 19...166, 13, 165556, 13, 16185, 175, 194, 9, 126, 7, 10, 13, 19...55561385, 195519, 2356, 13, 165135, 192, 71956655145, 19521555, 196, 13, 16555, 165, 196, 13, 162133, 56, 7, 10, 13, 15...5, 813172432, 5, 7, 8, 10...5, 65, 1656, 13, 165, 19195, 192, 3, 5, 7, 1913, 175, 195245124, 95215, 195, 1952410, 13, 19, 215595, 1916, 17117, 2455, 10, 1951717, 18, 2355, 18, 19, 23554, 19552, 5, 1955812562, 5, 1352, 5, 8, 136, 13165, 6, 13, 165555, 195, 19524196, 13, 161316, 17, 2413, 16, 175, 19555, 195, 12196, 13, 1655, 13, 17, 195, 195125132255, 19196, 7, 13, 16, 193, 7, 17566, 13, 1656, 13525165, 8135, 1955, 1913, 1955, 195, 7, 9, 13, 175, 13, 1952, 5, 1317, 24456, 13, 165, 195, 19192, 5, 8195, 15, 16, 1919556, 131055, 192, 3, 5, 1994458, 135, 195, 19165, 1914215, 194, 5, 12, 14, 17...162, 56, 13, 165, 1613, 24132, 5, 162, 5, 19545, 14, 19, 201213, 175, 12, 195, 19175, 1356, 13, 16, 175, 19, 235, 1417, 2455, 195, 195, 17, 196, 13, 1655, 1985, 195, 1355, 195, 195, 135, 196, 13, 164, 9, 185, 1921556, 13, 1655, 195555126, 13, 165, 192, 5-7, 15...555, 191351752, 51213, 172, 5555, 194, 5, 146, 7, 13, 19106555216, 194, 18, 2319245, 195HIST1H1ECEBPDHIST1H2BBSMAD5BRMS1LSERTAD1HIST1H2BCSEMG2HIST1H2BITNFRSF17RBM12BEI24FBXO22TRIM22IKBIPNLRX1TP53I3HIST1H2BMBTG2TRIAP1CENPERPS27LPRKAB2PRKAB1CDKN1ASEL1LAENID2LRRFIP2PLK3ARRDC4ITPKCB3GNT2MEX3BLCE1EDAAM1MDM2ACTA2GADD45ACCP110CBLBGXYLT1HIST1H2BGTM7SF3TIGARRRM2BDCP1BITPR1PCDH8BLOC1S2COILPPM1DDDB2E2F8USP41HIST1H3DE2F7AMER1RAPGEF2TOPORSPTGER4PHLDA3DUSP14HIST1H2BN


Description

This pathway describes the transcriptomic biomarker TGx-DDI genotoxicity assay (consisting of 64 genes) developed to readily distinguish DNA damage-inducing (DDI) agents from non-DDI agents.

Abstract from the paper "Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs" by Li et al. (2017) published in PNAS:

Standard in vitro assays to assess genotoxicity frequently generate positive results that are subsequently found to be irrelevant for in vivo carcinogenesis and human cancer risk assessment. Currently used follow-up methods, such as animal testing, are expensive and time-consuming, and the development of approaches enabling more accurate mechanism-based risk assessment is essential. We developed an in vitro transcriptomic biomarker-based approach that provides a robust biomarker reflecting stress-signaling responses. The biomarker correctly identifies the vast majority of irrelevant genotoxicity results from in vitro chromosome damage assays. TGx-DDI, a multigene biomarker for DNA damage-inducing agents, is the first biomarker that not only shows convincing interlaboratory and intralaboratory reproducibility, but also performs accurately in a system suitable for high-throughput screening.

Try the New WikiPathways

View approved pathways at the new wikipathways.org.

Quality Tags

Ontology Terms

 

Bibliography

View all...
  1. Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D; ''Large-scale mapping of human protein-protein interactions by mass spectrometry.''; Mol Syst Biol, 2007 PubMed Europe PMC Scholia
  2. Wang IX, Ramrattan G, Cheung VG; ''Genetic variation in insulin-induced kinase signaling.''; Mol Syst Biol, 2015 PubMed Europe PMC Scholia
  3. Wu X, Wang J, Cui X, Maianu L, Rhees B, Rosinski J, So WV, Willi SM, Osier MV, Hill HS, Page GP, Allison DB, Martin M, Garvey WT; ''The effect of insulin on expression of genes and biochemical pathways in human skeletal muscle.''; Endocrine, 2007 PubMed Europe PMC Scholia
  4. Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA; ''Stereotyped and specific gene expression programs in human innate immune responses to bacteria.''; Proc Natl Acad Sci U S A, 2002 PubMed Europe PMC Scholia
  5. Smirnov DA, Morley M, Shin E, Spielman RS, Cheung VG; ''Genetic analysis of radiation-induced changes in human gene expression.''; Nature, 2009 PubMed Europe PMC Scholia
  6. Noble CL, Abbas AR, Cornelius J, Lees CW, Ho GT, Toy K, Modrusan Z, Pal N, Zhong F, Chalasani S, Clark H, Arnott ID, Penman ID, Satsangi J, Diehl L; ''Regional variation in gene expression in the healthy colon is dysregulated in ulcerative colitis.''; Gut, 2008 PubMed Europe PMC Scholia
  7. Wang Q, Diskin S, Rappaport E, Attiyeh E, Mosse Y, Shue D, Seiser E, Jagannathan J, Shusterman S, Bansal M, Khazi D, Winter C, Okawa E, Grant G, Cnaan A, Zhao H, Cheung NK, Gerald W, London W, Matthay KK, Brodeur GM, Maris JM; ''Integrative genomics identifies distinct molecular classes of neuroblastoma and shows that multiple genes are targeted by regional alterations in DNA copy number.''; Cancer Res, 2006 PubMed Europe PMC Scholia
  8. Chen X, Cheung ST, So S, Fan ST, Barry C, Higgins J, Lai KM, Ji J, Dudoit S, Ng IO, Van De Rijn M, Botstein D, Brown PO; ''Gene expression patterns in human liver cancers.''; Mol Biol Cell, 2002 PubMed Europe PMC Scholia
  9. Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, Yeang CH, Angelo M, Ladd C, Reich M, Latulippe E, Mesirov JP, Poggio T, Gerald W, Loda M, Lander ES, Golub TR; ''Multiclass cancer diagnosis using tumor gene expression signatures.''; Proc Natl Acad Sci U S A, 2001 PubMed Europe PMC Scholia
  10. Bild AH, Yao G, Chang JT, Wang Q, Potti A, Chasse D, Joshi MB, Harpole D, Lancaster JM, Berchuck A, Olson JA Jr, Marks JR, Dressman HK, West M, Nevins JR; ''Oncogenic pathway signatures in human cancers as a guide to targeted therapies.''; Nature, 2006 PubMed Europe PMC Scholia
  11. Li HH, Chen R, Hyduke DR, Williams A, Frötschl R, Ellinger-Ziegelbauer H, O'Lone R, Yauk CL, Aubrecht J, Fornace AJ Jr; ''Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs.''; Proc Natl Acad Sci U S A, 2017 PubMed Europe PMC Scholia
  12. Johnson JM, Castle J, Garrett-Engele P, Kan Z, Loerch PM, Armour CD, Santos R, Schadt EE, Stoughton R, Shoemaker DD; ''Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays.''; Science, 2003 PubMed Europe PMC Scholia
  13. Innocenti F, Cooper GM, Stanaway IB, Gamazon ER, Smith JD, Mirkov S, Ramirez J, Liu W, Lin YS, Moloney C, Aldred SF, Trinklein ND, Schuetz E, Nickerson DA, Thummel KE, Rieder MJ, Rettie AE, Ratain MJ, Cox NJ, Brown CD; ''Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue.''; PLoS Genet, 2011 PubMed Europe PMC Scholia
  14. Perou CM, Sørlie T, Eisen MB, van de Rijn M, Jeffrey SS, Rees CA, Pollack JR, Ross DT, Johnsen H, Akslen LA, Fluge O, Pergamenschikov A, Williams C, Zhu SX, Lønning PE, Børresen-Dale AL, Brown PO, Botstein D; ''Molecular portraits of human breast tumours.''; Nature, 2000 PubMed Europe PMC Scholia
  15. Wu G, Feng X, Stein L; ''A human functional protein interaction network and its application to cancer data analysis.''; Genome Biol, 2010 PubMed Europe PMC Scholia
  16. Mallon BS, Chenoweth JG, Johnson KR, Hamilton RS, Tesar PJ, Yavatkar AS, Tyson LJ, Park K, Chen KG, Fann YC, McKay RD; ''StemCellDB: the human pluripotent stem cell database at the National Institutes of Health.''; Stem Cell Res, 2013 PubMed Europe PMC Scholia
  17. Roth RB, Hevezi P, Lee J, Willhite D, Lechner SM, Foster AC, Zlotnik A; ''Gene expression analyses reveal molecular relationships among 20 regions of the human CNS.''; Neurogenetics, 2006 PubMed Europe PMC Scholia
  18. Rosenwald A, Alizadeh AA, Widhopf G, Simon R, Davis RE, Yu X, Yang L, Pickeral OK, Rassenti LZ, Powell J, Botstein D, Byrd JC, Grever MR, Cheson BD, Chiorazzi N, Wilson WH, Kipps TJ, Brown PO, Staudt LM; ''Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia.''; J Exp Med, 2001 PubMed Europe PMC Scholia
  19. Rieger KE, Hong WJ, Tusher VG, Tang J, Tibshirani R, Chu G; ''Toxicity from radiation therapy associated with abnormal transcriptional responses to DNA damage.''; Proc Natl Acad Sci U S A, 2004 PubMed Europe PMC Scholia
  20. Chen TC, Lin KT, Chen CH, Lee SA, Lee PY, Liu YW, Kuo YL, Wang FS, Lai JM, Huang CY; ''Using an in situ proximity ligation assay to systematically profile endogenous protein-protein interactions in a pathway network.''; J Proteome Res, 2014 PubMed Europe PMC Scholia
  21. Burington B, Barlogie B, Zhan F, Crowley J, Shaughnessy JD Jr; ''Tumor cell gene expression changes following short-term in vivo exposure to single agent chemotherapeutics are related to survival in multiple myeloma.''; Clin Cancer Res, 2008 PubMed Europe PMC Scholia
  22. Taipale M, Tucker G, Peng J, Krykbaeva I, Lin ZY, Larsen B, Choi H, Berger B, Gingras AC, Lindquist S; ''A quantitative chaperone interaction network reveals the architecture of cellular protein homeostasis pathways.''; Cell, 2014 PubMed Europe PMC Scholia
  23. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM; ''Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling.''; Nature, 2000 PubMed Europe PMC Scholia
  24. Bahr TM, Hughes GJ, Armstrong M, Reisdorph R, Coldren CD, Edwards MG, Schnell C, Kedl R, LaFlamme DJ, Reisdorph N, Kechris KJ, Bowler RP; ''Peripheral blood mononuclear cell gene expression in chronic obstructive pulmonary disease.''; Am J Respir Cell Mol Biol, 2013 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
97441view22:09, 17 May 2018Linda.RieswijkReorganized and fixed unconnected lines
97398view21:01, 14 May 2018Linda.RieswijkFixed unconnected lines
97359view19:24, 10 May 2018Linda.RieswijkOntology Term : 'DNA damage response pathway' added !
97358view19:21, 10 May 2018Linda.RieswijkModified description
97355view19:02, 10 May 2018Linda.RieswijkModified description
97354view19:01, 10 May 2018Linda.RieswijkModified description
97352view18:58, 10 May 2018Linda.RieswijkNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
ACTA2GeneProduct59 (Entrez Gene)
AENGeneProduct64782 (Entrez Gene)
AMER1GeneProduct139285 (Entrez Gene)
ARRDC4GeneProduct91947 (Entrez Gene)
B3GNT2GeneProduct10678 (Entrez Gene)
BLOC1S2GeneProduct282991 (Entrez Gene)
BRMS1LGeneProduct84312 (Entrez Gene)
BTG2GeneProduct7832 (Entrez Gene)
CBLBGeneProduct868 (Entrez Gene)
CCP110GeneProduct9738 (Entrez Gene)
CDKN1AGeneProduct1026 (Entrez Gene)
CEBPDGeneProduct1052 (Entrez Gene)
CENPEGeneProduct1062 (Entrez Gene)
COILGeneProduct8161 (Entrez Gene)
DAAM1GeneProduct23002 (Entrez Gene)
DCP1BGeneProduct196513 (Entrez Gene)
DDB2GeneProduct1643 (Entrez Gene)
DUSP14GeneProduct11072 (Entrez Gene)
E2F7GeneProduct144455 (Entrez Gene)
E2F8GeneProduct79733 (Entrez Gene)
EI24GeneProduct9538 (Entrez Gene)
FBXO22GeneProduct26263 (Entrez Gene)
GADD45AGeneProduct1647 (Entrez Gene)
GXYLT1GeneProduct283464 (Entrez Gene)
HIST1H1EGeneProduct3008 (Entrez Gene)
HIST1H2BBGeneProduct3018 (Entrez Gene)
HIST1H2BCGeneProduct8347 (Entrez Gene)
HIST1H2BGGeneProduct8339 (Entrez Gene)
HIST1H2BIGeneProduct8346 (Entrez Gene)
HIST1H2BMGeneProduct8342 (Entrez Gene)
HIST1H2BNGeneProduct8341 (Entrez Gene)
HIST1H3DGeneProduct8351 (Entrez Gene)
ID2GeneProduct3398 (Entrez Gene)
IKBIPGeneProduct121457 (Entrez Gene)
ITPKCGeneProduct80271 (Entrez Gene)
ITPR1GeneProduct3708 (Entrez Gene)
LCE1EGeneProduct353135 (Entrez Gene)
LRRFIP2GeneProduct9209 (Entrez Gene)
MDM2GeneProduct4193 (Entrez Gene)
MEX3BGeneProduct84206 (Entrez Gene)
NLRX1GeneProduct79671 (Entrez Gene) Type your comment here
PCDH8GeneProduct5100 (Entrez Gene)
PHLDA3GeneProduct23612 (Entrez Gene)
PLK3GeneProduct1263 (Entrez Gene)
PPM1DGeneProduct8493 (Entrez Gene)
PRKAB1GeneProduct5564 (Entrez Gene)
PRKAB2GeneProduct5565 (Entrez Gene)
PTGER4GeneProduct5734 (Entrez Gene)
RAPGEF2GeneProduct9693 (Entrez Gene)
RBM12BGeneProduct389677 (Entrez Gene)
RPS27LGeneProduct6232 (Entrez Gene) Type your comment here
RRM2BGeneProduct50484 (Entrez Gene)
SEL1LGeneProduct6400 (Entrez Gene)
SEMG2GeneProduct6407 (Entrez Gene)
SERTAD1GeneProduct29950 (Entrez Gene)
SMAD5GeneProduct4090 (Entrez Gene)
TIGARGeneProduct57103 (Entrez Gene)
TM7SF3GeneProduct51768 (Entrez Gene)
TNFRSF17GeneProduct608 (Entrez Gene)
TOPORSGeneProduct10210 (Entrez Gene)
TP53I3GeneProduct9540 (Entrez Gene)
TRIAP1GeneProduct51499 (Entrez Gene)
TRIM22GeneProduct10346 (Entrez Gene)
USP41GeneProduct373856 (Entrez Gene)

Annotated Interactions

No annotated interactions

Retrieved from "https://classic.wikipathways.org/index.php/Pathway:WP4286"
Personal tools