Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types
Meng X, Wang J, Yuan C, Li X, Zhou Y, Hofestädt R, Chen M (2015)
Oncogenesis 4(12): e177.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Meng, X.;
Wang, J.;
Yuan, C.;
Li, X.;
Zhou, Y.;
Hofestädt, RalfUniBi;
Chen, M.
Einrichtung
Abstract / Bemerkung
Protein-protein interactions (PPIs) and microRNA (miRNA)-target interactions are important for deciphering the mechanisms of tumorigenesis. However, current PPI databases do not support cancer-specific analysis. Also, no available databases can be used to retrieve cancer-associated miRNA-target interactions. As the pathogenesis of human cancers is affected by several miRNAs rather than a single miRNA, it is needed to uncover miRNA synergism in a systems level. Here for each cancer type, we constructed a miRNA-miRNA functionally synergistic network based on the functions of miRNA targets and their topological features in that cancer PPI network. And for the first time, we report the cancer-specific database CancerNet (http://bis.zju.edu.cn/CancerNet), which contains information about PPIs, miRNA-target interactions and functionally synergistic miRNA-miRNA pairs across 33 human cancer types. In addition, PPI information across 33 main normal tissues and cell types are included. Flexible query methods are allowed to retrieve cancer molecular interactions. Network viewer can be used to visualize interactions that users are interested in. Enrichment analysis tool was designed to detect significantly overrepresented Gene Ontology categories of miRNA targets. Thus, CancerNet serves as a comprehensive platform for assessing the roles of proteins and miRNAs, as well as their interactions across human cancers.
Erscheinungsjahr
2015
Zeitschriftentitel
Oncogenesis
Band
4
Ausgabe
12
Art.-Nr.
e177
ISSN
2157-9024
Page URI
https://pub.uni-bielefeld.de/record/2901356
Zitieren
Meng X, Wang J, Yuan C, et al. Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types. Oncogenesis. 2015;4(12): e177.
Meng, X., Wang, J., Yuan, C., Li, X., Zhou, Y., Hofestädt, R., & Chen, M. (2015). Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types. Oncogenesis, 4(12), e177. doi:10.1038/oncsis.2015.40
Meng, X., Wang, J., Yuan, C., Li, X., Zhou, Y., Hofestädt, Ralf, and Chen, M. 2015. “Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types”. Oncogenesis 4 (12): e177.
Meng, X., Wang, J., Yuan, C., Li, X., Zhou, Y., Hofestädt, R., and Chen, M. (2015). Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types. Oncogenesis 4:e177.
Meng, X., et al., 2015. Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types. Oncogenesis, 4(12): e177.
X. Meng, et al., “Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types”, Oncogenesis, vol. 4, 2015, : e177.
Meng, X., Wang, J., Yuan, C., Li, X., Zhou, Y., Hofestädt, R., Chen, M.: Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types. Oncogenesis. 4, : e177 (2015).
Meng, X., Wang, J., Yuan, C., Li, X., Zhou, Y., Hofestädt, Ralf, and Chen, M. “Cancernet: a database for decoding multilevel molecular interactions across diverse cancer types”. Oncogenesis 4.12 (2015): e177.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
8 Zitationen in Europe PMC
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Rao PK, Missiaglia E, Shields L, Hyde G, Yuan B, Shepherd CJ, Shipley J, Lodish HF., FASEB J. 24(9), 2010
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Nohata N, Hanazawa T, Kikkawa N, Sakurai D, Sasaki K, Chiyomaru T, Kawakami K, Yoshino H, Enokida H, Nakagawa M, Okamoto Y, Seki N., Int. J. Oncol. 39(5), 2011
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The tumour-suppressive function of miR-1 and miR-133a targeting TAGLN2 in bladder cancer.
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Chen WS, Leung CM, Pan HW, Hu LY, Li SC, Ho MR, Tsai KW., Oncol. Rep. 28(3), 2012
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Caruso S, Bazan V, Rolfo C, Insalaco L, Fanale D, Bronte G, Corsini LR, Rizzo S, Cicero G, Russo A., Oncogenesis 1(), 2012
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Down-regulation of micro-RNA-1 (miR-1) in lung cancer. Suppression of tumorigenic property of lung cancer cells and their sensitization to doxorubicin-induced apoptosis by miR-1.
Nasser MW, Datta J, Nuovo G, Kutay H, Motiwala T, Majumder S, Wang B, Suster S, Jacob ST, Ghoshal K., J. Biol. Chem. 283(48), 2008
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Kawakami K, Enokida H, Chiyomaru T, Tatarano S, Yoshino H, Kagara I, Gotanda T, Tachiwada T, Nishiyama K, Nohata N, Seki N, Nakagawa M., Eur. J. Cancer 48(6), 2012
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Han C, Zhou Y, An Q, Li F, Li D, Zhang X, Yu Z, Zheng L, Duan Z, Kan Q., Tumour Biol. 36(9), 2015
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miR-133 is a key negative regulator of CDC42-PAK pathway in gastric cancer.
Cheng Z, Liu F, Wang G, Li Y, Zhang H, Li F., Cell. Signal. 26(12), 2014
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Cheng Z, Liu F, Wang G, Li Y, Zhang H, Li F., Cell. Signal. 26(12), 2014
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Tumour suppressors miR-1 and miR-133a target the oncogenic function of purine nucleoside phosphorylase (PNP) in prostate cancer.
Kojima S, Chiyomaru T, Kawakami K, Yoshino H, Enokida H, Nohata N, Fuse M, Ichikawa T, Naya Y, Nakagawa M, Seki N., Br. J. Cancer 106(2), 2011
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Integrative analysis of miRNA and mRNA expression profiles in pheochromocytoma and paraganglioma identifies genotype-specific markers and potentially regulated pathways.
de Cubas AA, Leandro-Garcia LJ, Schiavi F, Mancikova V, Comino-Mendez I, Inglada-Perez L, Perez-Martinez M, Ibarz N, Ximenez-Embun P, Lopez-Jimenez E, Maliszewska A, Leton R, Gomez Grana A, Bernal C, Alvarez-Escola C, Rodriguez-Antona C, Opocher G, Munoz J, Megias D, Cascon A, Robledo M., Endocr. Relat. Cancer 20(4), 2013
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Identification of microRNA expression patterns in cutaneous and uveal melanoma cell lines.
Venza M, Dell'Aversana C, Visalli M, Altucci L, Teti D, Venza I., Tumori 100(1), 2014
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Four microRNAs promote prostate cell proliferation with regulation of PTEN and its downstream signals in vitro.
Tian L, Fang YX, Xue JL, Chen JZ., PLoS ONE 8(9), 2013
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Tian L, Fang YX, Xue JL, Chen JZ., PLoS ONE 8(9), 2013
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miR-30 as a tumor suppressor connects EGF/Src signal to ERG and EMT.
Kao CJ, Martiniez A, Shi XB, Yang J, Evans CP, Dobi A, deVere White RW, Kung HJ., Oncogene 33(19), 2013
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Kao CJ, Martiniez A, Shi XB, Yang J, Evans CP, Dobi A, deVere White RW, Kung HJ., Oncogene 33(19), 2013
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Upregulation of miR-96 enhances cellular proliferation of prostate cancer cells through FOXO1.
Haflidadottir BS, Larne O, Martin M, Persson M, Edsjo A, Bjartell A, Ceder Y., PLoS ONE 8(8), 2013
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Identification of miR-133b and RB1CC1 as independent predictors for biochemical recurrence and potential therapeutic targets for prostate cancer.
Li X, Wan X, Chen H, Yang S, Liu Y, Mo W, Meng D, Du W, Huang Y, Wu H, Wang J, Li T, Li Y., Clin. Cancer Res. 20(9), 2014
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miR-141 modulates androgen receptor transcriptional activity in human prostate cancer cells through targeting the small heterodimer partner protein.
Xiao J, Gong AY, Eischeid AN, Chen D, Deng C, Young CY, Chen XM., Prostate 72(14), 2012
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RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome.
Li B, Dewey CN., BMC Bioinformatics 12(), 2011
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Li B, Dewey CN., BMC Bioinformatics 12(), 2011
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Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution.
Bradley RK, Merkin J, Lambert NJ, Burge CB., PLoS Biol. 10(1), 2012
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TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL., Genome Biol. 14(4), 2013
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Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL., Genome Biol. 14(4), 2013
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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L., Nat. Biotechnol. 28(5), 2010
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Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L., Nat. Biotechnol. 28(5), 2010
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The BioGRID Interaction Database: 2011 update.
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The Database of Interacting Proteins: 2004 update.
Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D., Nucleic Acids Res. 32(Database issue), 2004
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Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D., Nucleic Acids Res. 32(Database issue), 2004
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Human Protein Reference Database--2009 update.
Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A., Nucleic Acids Res. 37(Database issue), 2008
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PMID: 18988627
The IntAct molecular interaction database in 2012.
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H., Nucleic Acids Res. 40(Database issue), 2011
PMID: 22121220
Kerrien S, Aranda B, Breuza L, Bridge A, Broackes-Carter F, Chen C, Duesbury M, Dumousseau M, Feuermann M, Hinz U, Jandrasits C, Jimenez RC, Khadake J, Mahadevan U, Masson P, Pedruzzi I, Pfeiffenberger E, Porras P, Raghunath A, Roechert B, Orchard S, Hermjakob H., Nucleic Acids Res. 40(Database issue), 2011
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MINT, the molecular interaction database: 2012 update.
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miRBase: annotating high confidence microRNAs using deep sequencing data.
Kozomara A, Griffiths-Jones S., Nucleic Acids Res. 42(Database issue), 2013
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DIANA-microT web server: elucidating microRNA functions through target prediction.
Maragkakis M, Reczko M, Simossis VA, Alexiou P, Papadopoulos GL, Dalamagas T, Giannopoulos G, Goumas G, Koukis E, Kourtis K, Vergoulis T, Koziris N, Sellis T, Tsanakas P, Hatzigeorgiou AG., Nucleic Acids Res. 37(Web Server issue), 2009
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miRDB: an online resource for microRNA target prediction and functional annotations.
Wong N, Wang X., Nucleic Acids Res. 43(Database issue), 2014
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The role of site accessibility in microRNA target recognition.
Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E., Nat. Genet. 39(10), 2007
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RNAhybrid: microRNA target prediction easy, fast and flexible.
Kruger J, Rehmsmeier M., Nucleic Acids Res. 34(Web Server issue), 2006
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Kruger J, Rehmsmeier M., Nucleic Acids Res. 34(Web Server issue), 2006
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Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.
Lewis BP, Burge CB, Bartel DP., Cell 120(1), 2005
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MicroRNA targets in Drosophila.
Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS., Genome Biol. 5(1), 2003
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miRecords: an integrated resource for microRNA-target interactions.
Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T., Nucleic Acids Res. 37(Database issue), 2008
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miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions.
Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel A, Chou CH, Chu CF, Huang HY, Lin CM, Ho SY, Jian TY, Lin FM, Chang TH, Weng SL, Liao KW, Liao IE, Liu CC, Huang HD., Nucleic Acids Res. 42(Database issue), 2013
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The Gene Ontology in 2010: extensions and refinements.
Gene Ontology Consortium, Berardini TZ, Li D, Huala E, Bridges S, Burgess S, McCarthy F, Carbon S, Lewis SE, Mungall CJ, Abdulla A, Wood V, Feltrin E, Valle G, Chisholm RL, Fey P, Gaudet P, Kibbe W, Basu S, Bushmanova Y, Eilbeck K, Siegele DA, McIntosh B, Renfro D, Zweifel A, Hu JC, Ashburner M, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Bairoch A, Barrell D, Binns D, Blatter MC, Bougueleret L, Boutet E, Breuza L, Bridge A, Browne P, Chan WM, Coudert E, Daugherty L, Dimmer E, Eberhardt R, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Foulger R, Gruaz-Gumowski N, Hinz U, Huntley R, Jimenez S, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, O'Donovan C, Pedruzzi I, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stanley E, Stutz A, Sundaram S, Tognolli M, Xenarios I, Harris MA, Deegan JI, Ireland A, Lomax J, Jaiswal P, Chibucos M, Giglio MG, Wortman J, Hannick L, Madupu R, Botstein D, Dolinski K, Livstone MS, Oughtred R, Blake JA, Bult C, Diehl AD, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Sitnikov D, Collmer C, Torto-Alalibo T, Laulederkind S, Shimoyama M, Twigger S, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Christie KR, Costanzo MC, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Aslett M, Chan J, Kishore R, Sternberg P, Van Auke K, Khodiyar VK, Lovering RC, Talmud PJ, Howe D, Westerfield M., Nucleic Acids Res. 38(Database issue), 2009
PMID: 19920128
Gene Ontology Consortium, Berardini TZ, Li D, Huala E, Bridges S, Burgess S, McCarthy F, Carbon S, Lewis SE, Mungall CJ, Abdulla A, Wood V, Feltrin E, Valle G, Chisholm RL, Fey P, Gaudet P, Kibbe W, Basu S, Bushmanova Y, Eilbeck K, Siegele DA, McIntosh B, Renfro D, Zweifel A, Hu JC, Ashburner M, Tweedie S, Alam-Faruque Y, Apweiler R, Auchinchloss A, Bairoch A, Barrell D, Binns D, Blatter MC, Bougueleret L, Boutet E, Breuza L, Bridge A, Browne P, Chan WM, Coudert E, Daugherty L, Dimmer E, Eberhardt R, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Foulger R, Gruaz-Gumowski N, Hinz U, Huntley R, Jimenez S, Jungo F, Keller G, Laiho K, Legge D, Lemercier P, Lieberherr D, Magrane M, O'Donovan C, Pedruzzi I, Poux S, Rivoire C, Roechert B, Sawford T, Schneider M, Stanley E, Stutz A, Sundaram S, Tognolli M, Xenarios I, Harris MA, Deegan JI, Ireland A, Lomax J, Jaiswal P, Chibucos M, Giglio MG, Wortman J, Hannick L, Madupu R, Botstein D, Dolinski K, Livstone MS, Oughtred R, Blake JA, Bult C, Diehl AD, Dolan M, Drabkin H, Eppig JT, Hill DP, Ni L, Ringwald M, Sitnikov D, Collmer C, Torto-Alalibo T, Laulederkind S, Shimoyama M, Twigger S, D'Eustachio P, Matthews L, Balakrishnan R, Binkley G, Cherry JM, Christie KR, Costanzo MC, Engel SR, Fisk DG, Hirschman JE, Hitz BC, Hong EL, Krieger CJ, Miyasato SR, Nash RS, Park J, Skrzypek MS, Weng S, Wong ED, Aslett M, Chan J, Kishore R, Sternberg P, Van Auke K, Khodiyar VK, Lovering RC, Talmud PJ, Howe D, Westerfield M., Nucleic Acids Res. 38(Database issue), 2009
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Using information content to evaluate semantic similarity in a taxonomy
AUTHOR UNKNOWN, 1995
AUTHOR UNKNOWN, 1995
Community structure in social and biological networks.
Girvan M, Newman ME., Proc. Natl. Acad. Sci. U.S.A. 99(12), 2002
PMID: 12060727
Girvan M, Newman ME., Proc. Natl. Acad. Sci. U.S.A. 99(12), 2002
PMID: 12060727
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