Pathprinting: An integrative approach to understand the functional basis of disease

Genome Medicine

Volumn 5, Issue 7, 2013, Pages

  Altschuler, Gabriel M ^a   Hofmann, Oliver ^a,d   Kalatskaya, Irina ^b   Payne, Rebecca ^a   Ho Sui, Shannan J ^a   Saxena, Uma ^a   Krivtsov, Andrei V ^c   Armstrong, Scott A ^c,d   Cai, Tianxi ^a   Stein, Lincoln ^b   Hide, Winston A ^a,d  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b ONTARIO INSTITUTE FOR CANCER RESEARCH   (Canada)

^c BOSTON CHILDREN S HOSPITAL   (United States)

^d HARVARD STEM CELL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; PHOSPHATIDYLINOSITOL 4,5 BISPHOSPHATE PHOSPHODIESTERASE; PHOSPHATIDYLINOSITOL 4,5 BISPHOSPHATE PHOSPHODIESTERASE GAMMA 2; RAN PROTEIN; UNCLASSIFIED DRUG;

ACUTE GRANULOCYTIC LEUKEMIA; ANIMAL TISSUE; ARTICLE; BRAIN TISSUE; CAENORHABDITIS ELEGANS; CANCER PROGNOSIS; CONTROLLED STUDY; DNA REPLICATION; DROSOPHILA MELANOGASTER; EMBRYONIC STEM CELL; G1 PHASE CELL CYCLE CHECKPOINT; GENE EXPRESSION; GENE EXPRESSION PROFILING; HUMAN; HUMAN TISSUE; KIDNEY PARENCHYMA; LIVER PARENCHYMA; LUNG PARENCHYMA; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PATHPRINTING; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; RAT; S PHASE CELL CYCLE CHECKPOINT; SIGNAL TRANSDUCTION; SKELETAL MUSCLE; SPLEEN; STEM CELL; WNT SIGNALING PATHWAY; ZEBRA FISH;

EID: 84880953958     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm472     Document Type: Article

References (57)

1. Wang X, Gulbahce N, Yu H. Network-based methods for human disease gene prediction. Brief Funct Genomics 2011, 10:280-293. 10.1093/bfgp/elr024, 21764832.
2. Liu Y, Koyuturk M, Barnholtz-Sloan JS, Chance MR. Gene interaction enrichment and network analysis to identify dysregulated pathways and their interactions in complex diseases. BMC Syst Biol 2012, 6:65. 10.1186/1752-0509-6-65, 3426489, 22694839.
3. Yang X. Use of functional genomics to identify candidate genes underlying human genetic association studies of vascular diseases. Arterioscler Thromb Vasc Biol 2012, 32:216-222. 10.1161/ATVBAHA.111.232702, 22258904.
4. Yang X, Zhang B, Zhu J. Functional genomics- and network-driven systems biology approaches for pharmacogenomics and toxicogenomics. Curr Drug Metab 2012, 13:952-967. 10.2174/138920012802138633, 22591344.
5. Ala U, Piro RM, Grassi E, Damasco C, Silengo L, Oti M, Provero P, Di Cunto F. Prediction of human disease genes by human-mouse conserved coexpression analysis. PLoS Comput Biol 2008, 4:e1000043. 10.1371/journal.pcbi.1000043, 2268251, 18369433.
6. Le H-S, Oltvai ZN, Bar-Joseph Z. Cross species queries of large gene expression databases. Bioinformatics 2010, 28:2349-2356.
7. Sweet-Cordero A, Mukherjee S, Subramanian A, You H, Roix JJ, Ladd-Acosta C, Mesirov J, Golub TR, Jacks T. An oncogenic KRAS2 expression signature identified by cross-species gene-expression analysis. Nat Genet 2005, 37:48-55.
8. Sadanandam A, Futakuchi M, Lyssiotis CA, Gibb WJ, Singh RK. A cross-species analysis of a mouse model of breast cancer-specific osteolysis and human bone metastases using gene expression profiling. BMC Cancer 2011, 11:304. 10.1186/1471-2407-11-304, 3171728, 21774828.
9. Johnson RA, Wright KD, Poppleton H, Mohankumar KM, Finkelstein D, Pounds SB, Rand V, Leary SE, White E, Eden C, Hogg T, Northcott P, Mack S, Neale G, Wang YD, Coyle B, Atkinson J, DeWire M, Kranenburg TA, Gillespie Y, Allen JC, Merchant T, Boop FA, Sanford RA, Gajjar A, Ellison DW, Taylor MD, Grundy RG, Gilbertson RJ. Cross-species genomics matches driver mutations and cell compartments to model ependymoma. Nature 2010, 466:632-636. 10.1038/nature09173, 2912966, 20639864.
10. Barrett T, Troup DB, Wilhite SE, Ledoux P, Rudnev D, Evangelista C, Kim IF, Soboleva A, Tomashevsky M, Edgar R. NCBI GEO: mining tens of millions of expression profiles--database and tools update. Nucleic Acids Res 2007, 35:D760-765. 10.1093/nar/gkl887, 1669752, 17099226.
11. Rustici G, Kolesnikov N, Brandizi M, Burdett T, Dylag M, Emam I, Farne A, Hastings E, Ison J, Keays M, Kurbatova N, Malone J, Mani R, Mupo A, Pedro Pereira R, Pilicheva E, Rung J, Sharma A, Tang YA, Ternent T, Tikhonov A, Welter D, Williams E, Brazma A, Parkinson H, Sarkans U. ArrayExpress update--trends in database growth and links to data analysis tools. Nucleic Acids Res 2013, 41:D987-990. 10.1093/nar/gks1174, 3531147, 23193272.
12. Engreitz JM, Morgan AA, Dudley JT, Chen R, Thathoo R, Altman RB, Butte AJ. Content-based microarray search using differential expression profiles. BMC Bioinformatics 2010, 11:603. 10.1186/1471-2105-11-603, 3022631, 21172034.
13. Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P. CellMontage: similar expression profile search server. Bioinformatics 2007, 23:3103-3104. 10.1093/bioinformatics/btm462, 17895274.
14. Keum C, Woo JH, Oh WS, Park S-N, No KT. Improving gene expression similarity measurement using pathway-based analytic dimension. BMC Genomics 2009, 10(Suppl 3):S15. 10.1186/1471-2164-10-S3-S15, 2788367, 19958478.
15. McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA. The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. Nucleic Acids Res 2011, 39:D1011-1015. 10.1093/nar/gkq1259, 3013751, 21177656.
16. Seita J, Sahoo D, Rossi DJ, Bhattacharya D, Serwold T, Inlay MA, Ehrlich LI, Fathman JW, Dill DL, Weissman IL. Gene expression commons: an open platform for absolute gene expression profiling. PLoS ONE 2012, 7:e40321. 10.1371/journal.pone.0040321, 3399844, 22815738.
17. Li Z, Su Z, Wen Z, Shi L, Chen T. Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles. BMC Bioinformatics 2009, 10(Suppl 11):S12. 10.1186/1471-2105-10-S11-S12, 2788352, 19958511.
18. Croft D, O'Kelly G, Wu G, Haw R, Gillespie M, Matthews L, Caudy M, Garapati P, Gopinath G, Jassal B, Jupe S, Kalatskaya I, Mahajan S, May B, Ndegwa N, Schmidt E, Shamovsky V, Yung C, Birney E, Hermjakob H, D'Eustachio P, Stein L. Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res 2011, 39:D691-697. 10.1093/nar/gkq1018, 3013646, 21067998.
19. Kanehisa M, Goto S, Furumichi M, Tanabe M, Hirakawa M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res 2010, 38:D355-360. 10.1093/nar/gkp896, 2808910, 19880382.
20. Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol 2008, 6:e184. 10.1371/journal.pbio.0060184, 2475545, 18651794.
21. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
22. Gatza ML, Lucas JE, Barry WT, Kim JW, Wang Q, Crawford MD, Datto MB, Kelley M, Mathey-Prevot B, Potti A, Nevins JR. A pathway-based classification of human breast cancer. Proc Natl Acad Sci USA 2010, 107:6994-6999. 10.1073/pnas.0912708107, 2872436, 20335537.
23. Greenblum SI, Efroni S, Schaefer CF, Buetow KH. The PathOlogist: an automated tool for pathway-centric analysis. BMC bioinformatics 2011, 12:133. 10.1186/1471-2105-12-133, 3098789, 21542931.
24. Gundem G, Lopez-Bigas N. Sample-level enrichment analysis unravels shared stress phenotypes among multiple cancer types. Genome Med 2012, 4:28. 10.1186/gm327, 3446278, 22458606.
25. Verhaak RG, Hoadley KA, Purdom E, Wang V, Qi Y, Wilkerson MD, Miller CR, Ding L, Golub T, Mesirov JP, Alexe G, Lawrence M, O'Kelly M, Tamayo P, Weir BA, Gabriel S, Winckler W, Gupta S, Jakkula L, Feiler HS, Hodgson JG, James CD, Sarkaria JN, Brennan C, Kahn A, Spellman PT, Wilson RK, Speed TP, Gray JW, Meyerson M, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell 2010, 17:98-110. 10.1016/j.ccr.2009.12.020, 2818769, 20129251.
26. Lee E, Chuang HY, Kim JW, Ideker T, Lee D. Inferring pathway activity toward precise disease classification. PLoS Comput Biol 2008, 4:e1000217. 10.1371/journal.pcbi.1000217, 2563693, 18989396.
27. Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
28. Chen R, Li L, Butte AJ. AILUN: reannotating gene expression data automatically. Nat Methods 2007, 4:879. 10.1038/nmeth1107-879, 2716375, 17971777.
29. Burgess DJ. Alternative splicing: proteomic rewiring through transcriptomic diversity. Nat Rev Genet 2012, 13:518-519.
30. Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GSS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HKC, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TSK, Lin J-X, Houtman JCD, Desiderio S, Renauld J-C, Constantinescu SN, et al. NetPath: a public resource of curated signal transduction pathways. Genome Biol 2010, 11:R3. 10.1186/gb-2010-11-1-r3, 2847715, 20067622.
31. Wu G, Feng X, Stein L. A human functional protein interaction network and its application to cancer data analysis. Genome Biol 2010, 11:R53. 10.1186/gb-2010-11-5-r53, 2898064, 20482850.
32. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, Dicuccio M, Federhen S, Feolo M, Fingerman IM, Geer LY, Helmberg W, Kapustin Y, Krasnov S, Landsman D, Lipman DJ, Lu Z, Madden TL, Madej T, Maglott DR, Marchler-Bauer A, Miller V, Karsch-Mizrachi I, Ostell J, Panchenko A, Phan L, Pruitt KD, Schuler GD, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2012, 40:D13-25. 10.1093/nar/gkr1184, 3245031, 22140104.
33. Altenhoff AM, Dessimoz C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput Biol 2009, 5:e1000262. 10.1371/journal.pcbi.1000262, 2612752, 19148271.
34. Ackermann M, Strimmer K. A general modular framework for gene set enrichment analysis. BMC Bioinformatics 2009, 10:47. 10.1186/1471-2105-10-47, 2661051, 19192285.
35. Tian L, Greenberg SA, Kong SW, Altschuler J, Kohane IS, Park PJ. Discovering statistically significant pathways in expression profiling studies. Proc Natl Acad Sci USA 2005, 102:13544-13549. 10.1073/pnas.0506577102, 1200092, 16174746.
36. Gatti DM, Barry WT, Nobel AB, Rusyn I, Wright FA. Heading down the wrong pathway: on the influence of correlation within gene sets. BMC Genomics 2010, 11:574. 10.1186/1471-2164-11-574, 3091509, 20955544.
37. Parmigiani G, Garrett ES, Anbazhagan R, Gabrielson E. A statistical framework for expression - based molecular classification in cancer. J R Stat Soc Series B Stat Methodol 2002, 64:717-736.
38. Choi H, Shen R, Chinnaiyan AM, Ghosh D. A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments. BMC Bioinformatics 2007, 8:364. 10.1186/1471-2105-8-364, 2246152, 17900369.
39. Molecular Brain. http://molecularbrain.org
40. Novershtern N, Subramanian A, Lawton LN, Mak RH, Haining WN, McConkey ME, Habib N, Yosef N, Chang CY, Shay T, Frampton GM, Drake AC, Leskov I, Nilsson B, Preffer F, Dombkowski D, Evans JW, Liefeld T, Smutko JS, Chen J, Friedman N, Young RA, Golub TR, Regev A, Ebert BL. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 2011, 144:96-309.
41. Chambers SM, Boles NC, Lin K-YK, Tierney MP, Bowman TV, Bradfute SB, Chen AJ, Merchant AA, Sirin O, Weksberg DC, Merchant MG, Fisk CJ, Shaw CA, Goodell MA. Hematopoietic fingerprints: an expression database of stem cells and their progeny. Cell Stem Cell 2007, 1:578-591. 10.1016/j.stem.2007.10.003, 2475548, 18371395.
42. Schliep K. Phylogenetics in R package phangorn. 2010, 1-46.
43. Pathprint. http://compbio.sph.harvard.edu/hidelab/pathprint
44. Koeva M, Forsberg EC, Stuart JM. Computational integration of homolog and pathway gene module expression reveals general stemness signatures. PLoS ONE 2011, 6:e18968. 10.1371/journal.pone.0018968, 3084730, 21559491.
45. Wang J, Alexander P, Wu L, Hammer R, Cleaver O, McKnight SL. Dependence of mouse embryonic stem cells on threonine catabolism. Science 2009, 325:435-439. 10.1126/science.1173288, 19589965.
46. Wei F, Scholer HR, Atchison ML. Sumoylation of Oct4 enhances its stability, DNA binding, and transactivation. J Biol Chem 2007, 282:21551-21560. 10.1074/jbc.M611041200, 17525163.
47. Painter MW, Davis S, Hardy RR, Mathis D, Benoist C. Transcriptomes of the B and T lineages compared by multiplatform microarray profiling. J Immunol 2011, 186:3047-3057. 10.4049/jimmunol.1002695, 3140206, 21307297.
48. Krivtsov AV, Twomey D, Feng Z, Stubbs MC, Wang Y, Faber J, Levine JE, Wang J, Hahn WC, Gilliland DG, Golub TR, Armstrong SA. Transformation from committed progenitor to leukaemia stem cell initiated by MLL-AF9. Nature 2006, 442:818-822. 10.1038/nature04980, 16862118.
49. Gentles AJ, Plevritis SK, Majeti R, Alizadeh AA. Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. JAMA 2010, 304:2706-2715. 10.1001/jama.2010.1862, 21177505.
50. Metzeler KH, Hummel M, Bloomfield CD, Spiekermann K, Braess J, Sauerland MC, Heinecke A, Radmacher M, Marcucci G, Whitman SP, Maharry K, Paschka P, Larson RA, Berdel WE, Buchner T, Wormann B, Mansmann U, Hiddemann W, Bohlander SK, Buske C. An 86-probe-set gene-expression signature predicts survival in cytogenetically normal acute myeloid leukemia. Blood 2008, 112:4193-4201. 10.1182/blood-2008-02-134411, 2954679, 18716133.
51. Stirewalt DL, Meshinchi S, Kopecky KJ, Fan W, Pogosova-Agadjanyan EL, Engel JH, Cronk MR, Dorcy KS, McQuary AR, Hockenbery D, Wood B, Heimfeld S, Radich JP. Identification of genes with abnormal expression changes in acute myeloid leukemia. Genes Chromosomes Cancer 2008, 47:8-20. 10.1002/gcc.20500, 17910043.
52. Tomasson MH, Xiang Z, Walgren R, Zhao Y, Kasai Y, Miner T, Ries RE, Lubman O, Fremont DH, McLellan MD, Payton JE, Westervelt P, DiPersio JF, Link DC, Walter MJ, Graubert TA, Watson M, Baty J, Heath S, Shannon WD, Nagarajan R, Bloomfield CD, Mardis ER, Wilson RK, Ley TJ. Somatic mutations and germline sequence variants in the expressed tyrosine kinase genes of patients with de novo acute myeloid leukemia. Blood 2008, 111:4797-4808. 10.1182/blood-2007-09-113027, 2343607, 18270328.
53. Wouters BJ, Lowenberg B, Erpelinck-Verschueren CA, van Putten WL, Valk PJ, Delwel R. Double CEBPA mutations, but not single CEBPA mutations, define a subgroup of acute myeloid leukemia with a distinctive gene expression profile that is uniquely associated with a favorable outcome. Blood 2009, 113:3088-3091. 10.1182/blood-2008-09-179895, 2662648, 19171880.
54. Assouline S, Culjkovic B, Cocolakis E, Rousseau C, Beslu N, Amri A, Caplan S, Leber B, Roy DC, Miller WH, Borden KL. Molecular targeting of the oncogene eIF4E in acute myeloid leukemia (AML): a proof-of-principle clinical trial with ribavirin. Blood 2009, 114:257-260. 10.1182/blood-2009-02-205153, 19433856.
55. Stem Cell Commons Stem Cell Commons., http://stemcellcommons.org
56. NHLBI Progenitor Cell Biology Consortium (PCBC). Bioinformatics and Genomics Tools. http://www.progenitorcells.org/content/bioinformatics-and-genomics-tools
57. Ho Sui SJ, Begley K, Reilly D, Chapman B, McGovern R, Rocca-Sera P, Maguire E, Altschuler GM, Hansen TA, Sompallae R, Krivtsov A, Shivdasani RA, Armstrong SA, Culhane AC, Correll M, Sansone SA, Hofmann O, Hide W. The Stem Cell Discovery Engine: an integrated repository and analysis system for cancer stem cell comparisons. Nucleic Acids Res 2012, 40:D984-991. 10.1093/nar/gkr1051, 3245064, 22121217.