Computational Systems Biology Methods and Protocols.7z

(nextflipdebug5) #1
Meyerson M, Sage J, Shendure J,
Schneider R, Buttner R, Wolf J, Nurnberg P,
Perner S, Heukamp LC, Brindle PK, Haas S,
Thomas RK (2012) Integrative genome ana-
lyses identify key somatic driver mutations of
small-cell lung cancer. Nat Genet 44
(10):1104–1110.https://doi.org/10.1038/
ng.2396


  1. Cancer Genome Atlas N (2012) Comprehen-
    sive molecular characterization of human
    colon and rectal cancer. Nature 487
    (7407):330–337.https://doi.org/10.1038/
    nature11252

  2. Cancer Genome Atlas Research N (2013)
    Comprehensive molecular characterization of
    clear cell renal cell carcinoma. Nature 499
    (7456):43–49. https://doi.org/10.1038/
    nature12222

  3. Cancer Genome Atlas Research N (2014)
    Comprehensive molecular characterization of
    gastric adenocarcinoma. Nature 513
    (7517):202–209.https://doi.org/10.1038/
    nature13480

  4. Cancer Genome Atlas Research N (2014)
    Comprehensive molecular characterization of
    urothelial bladder carcinoma. Nature 507
    (7492):315–322.https://doi.org/10.1038/
    nature12965

  5. Cancer Genome Atlas N (2015) Comprehen-
    sive genomic characterization of head and
    neck squamous cell carcinomas. Nature 517
    (7536):576–582.https://doi.org/10.1038/
    nature14129

  6. Cancer Genome Atlas Research N (2008)
    Comprehensive genomic characterization
    defines human glioblastoma genes and core
    pathways. Nature 455(7216):1061–1068.
    https://doi.org/10.1038/nature07385

  7. Cancer Genome Atlas Research N (2012)
    Comprehensive genomic characterization of
    squamous cell lung cancers. Nature 489
    (7417):519–525.https://doi.org/10.1038/
    nature11404

  8. Akbani R, Ng PK, Werner HM,
    Shahmoradgoli M, Zhang F, Ju Z, Liu W,
    Yang JY, Yoshihara K, Li J, Ling S, Seviour
    EG, Ram PT, Minna JD, Diao L, Tong P,
    Heymach JV, Hill SM, Dondelinger F,
    Stadler N, Byers LA, Meric-Bernstam F,
    Weinstein JN, Broom BM, Verhaak RG,
    Liang H, Mukherjee S, Lu Y, Mills GB
    (2014) A pan-cancer proteomic perspective
    on The Cancer Genome Atlas. Nat Commun
    5:3887. https://doi.org/10.1038/
    ncomms4887

  9. Ciriello G, Gatza ML, Beck AH, Wilkerson
    MD, Rhie SK, Pastore A, Zhang H,
    McLellan M, Yau C, Kandoth C, Bowlby R,


Shen H, Hayat S, Fieldhouse R, Lester SC,
Tse GM, Factor RE, Collins LC, Allison KH,
Chen YY, Jensen K, Johnson NB,
Oesterreich S, Mills GB, Cherniack AD,
Robertson G, Benz C, Sander C, Laird PW,
Hoadley KA, King TA, Network TR, Perou
CM (2015) Comprehensive molecular por-
traits of invasive lobular breast cancer. Cell
163(2):506–519.https://doi.org/10.1016/
j.cell.2015.09.033


  1. Cancer Genome Atlas N (2012) Comprehen-
    sive molecular portraits of human breast
    tumours. Nature 490(7418):61–70.https://
    doi.org/10.1038/nature11412

  2. Drake JM, Paull EO, Graham NA, Lee JK,
    Smith BA, Titz B, Stoyanova T, Faltermeier
    CM, Uzunangelov V, Carlin DE, Fleming
    DT, Wong CK, Newton Y, Sudha S, Vashisht
    AA, Huang J, Wohlschlegel JA, Graeber TG,
    Witte ON, Stuart JM (2016) Phosphopro-
    teome integration reveals patient-specific net-
    works in prostate cancer. Cell 166
    (4):1041–1054.https://doi.org/10.1016/j.
    cell.2016.07.007

  3. Cancer Genome Atlas Research N, Weinstein
    JN, Collisson EA, Mills GB, Shaw KR, Ozen-
    berger BA, Ellrott K, Shmulevich I, Sander C,
    Stuart JM (2013) The Cancer Genome Atlas
    Pan-Cancer analysis project. Nat Genet 45
    (10):1113–1120.https://doi.org/10.1038/
    ng.2764

  4. Neapolitan R, Horvath CM, Jiang X (2015)
    Pan-cancer analysis of TCGA data reveals
    notable signaling pathways. BMC Cancer
    15:516. https://doi.org/10.1186/s12885-
    015-1484-6

  5. Ruau D, Dudley JT, Chen R, Phillips NG,
    Swan GE, Lazzeroni LC, Clark JD, Butte
    AJ, Angst MS (2012) Integrative approach
    to pain genetics identifies pain sensitivity loci
    across diseases. PLoS Comput Biol 8(6):
    e1002538. https://doi.org/10.1371/jour
    nal.pcbi.1002538

  6. Liu P, Sanalkumar R, Bresnick EH, Keles S,
    Dewey CN (2016) Integrative analysis with
    ChIP-seq advances the limits of transcript
    quantification from RNA-seq. Genome Res
    26(8):1124–1133. https://doi.org/10.
    1101/gr.199174.115

  7. Knouf EC, Garg K, Arroyo JD, Correa Y,
    Sarkar D, Parkin RK, Wurz K, O’Briant KC,
    Godwin AK, Urban ND, Ruzzo WL,
    Gentleman R, Drescher CW, Swisher EM,
    Tewari M (2012) An integrative genomic
    approach identifies p73 and p63 as activators
    of miR-200 microRNA family transcription.
    Nucleic Acids Res 40(2):499–510.https://
    doi.org/10.1093/nar/gkr731


Integrative Analysis of Omics Big Data 133
Free download pdf