Literature DB >> 25246945

The 'dnet' approach promotes emerging research on cancer patient survival.

Hai Fang1, Julian Gough1.   

Abstract

We present the 'dnet' package and apply it to the 'TCGA' mutation and clinical data of >3,000 patients. We uncover the existence of an underlying gene network that at least partially controls cancer 'survivalness', with mutations that are significantly correlated with patient survival, yet independent of tumour origin and type. The survivalness network has natural community structure corresponding to tumour hallmarks, and contains genes that are potentially druggable in the clinic. This network has evolutionary roots in Deuterostomia identifying PTK2 and VAV1 as under-valued relative to more studied genes from that era. The 'dnet' R package is available at http://cran.r-project.org/package=dnet.

Entities:  

Year:  2014        PMID: 25246945      PMCID: PMC4160547          DOI: 10.1186/s13073-014-0064-8

Source DB:  PubMed          Journal:  Genome Med        ISSN: 1756-994X            Impact factor:   11.117


  35 in total

1.  Integration of biological networks and gene expression data using Cytoscape.

Authors:  Melissa S Cline; Michael Smoot; Ethan Cerami; Allan Kuchinsky; Nerius Landys; Chris Workman; Rowan Christmas; Iliana Avila-Campilo; Michael Creech; Benjamin Gross; Kristina Hanspers; Ruth Isserlin; Ryan Kelley; Sarah Killcoyne; Samad Lotia; Steven Maere; John Morris; Keiichiro Ono; Vuk Pavlovic; Alexander R Pico; Aditya Vailaya; Peng-Liang Wang; Annette Adler; Bruce R Conklin; Leroy Hood; Martin Kuiper; Chris Sander; Ilya Schmulevich; Benno Schwikowski; Guy J Warner; Trey Ideker; Gary D Bader
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

2.  Discovery of mutated subnetworks associated with clinical data in cancer.

Authors:  Fabio Vandin; Patrick Clay; Eli Upfal; Benjamin J Raphael
Journal:  Pac Symp Biocomput       Date:  2012

Review 3.  Gene-expression profiling in epithelial ovarian cancer.

Authors:  Panagiotis A Konstantinopoulos; Dimitrios Spentzos; Stephen A Cannistra
Journal:  Nat Clin Pract Oncol       Date:  2008-07-22

4.  Gene network-based cancer prognosis analysis with sparse boosting.

Authors:  Shuangge Ma; Yuan Huang; Jian Huang; Kuangnan Fang
Journal:  Genet Res (Camb)       Date:  2012-08       Impact factor: 1.588

Review 5.  Hallmarks of cancer: the next generation.

Authors:  Douglas Hanahan; Robert A Weinberg
Journal:  Cell       Date:  2011-03-04       Impact factor: 41.582

6.  DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more.

Authors:  Hai Fang; Julian Gough
Journal:  Nucleic Acids Res       Date:  2012-11-17       Impact factor: 16.971

7.  HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery.

Authors:  Alvin Leung; Gary D Bader; Jüri Reimand
Journal:  Bioinformatics       Date:  2014-04-08       Impact factor: 6.937

8.  Identifying functional modules in protein-protein interaction networks: an integrated exact approach.

Authors:  Marcus T Dittrich; Gunnar W Klau; Andreas Rosenwald; Thomas Dandekar; Tobias Müller
Journal:  Bioinformatics       Date:  2008-07-01       Impact factor: 6.937

9.  A domain-centric solution to functional genomics via dcGO Predictor.

Authors:  Hai Fang; Julian Gough
Journal:  BMC Bioinformatics       Date:  2013-02-28       Impact factor: 3.169

10.  Network-based survival analysis reveals subnetwork signatures for predicting outcomes of ovarian cancer treatment.

Authors:  Wei Zhang; Takayo Ota; Viji Shridhar; Jeremy Chien; Baolin Wu; Rui Kuang
Journal:  PLoS Comput Biol       Date:  2013-03-21       Impact factor: 4.475

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  34 in total

1.  Genomic analyses identify molecular subtypes of pancreatic cancer.

Authors:  Peter Bailey; David K Chang; Katia Nones; Amber L Johns; Ann-Marie Patch; Marie-Claude Gingras; David K Miller; Angelika N Christ; Tim J C Bruxner; Michael C Quinn; Craig Nourse; L Charles Murtaugh; Ivon Harliwong; Senel Idrisoglu; Suzanne Manning; Ehsan Nourbakhsh; Shivangi Wani; Lynn Fink; Oliver Holmes; Venessa Chin; Matthew J Anderson; Stephen Kazakoff; Conrad Leonard; Felicity Newell; Nick Waddell; Scott Wood; Qinying Xu; Peter J Wilson; Nicole Cloonan; Karin S Kassahn; Darrin Taylor; Kelly Quek; Alan Robertson; Lorena Pantano; Laura Mincarelli; Luis N Sanchez; Lisa Evers; Jianmin Wu; Mark Pinese; Mark J Cowley; Marc D Jones; Emily K Colvin; Adnan M Nagrial; Emily S Humphrey; Lorraine A Chantrill; Amanda Mawson; Jeremy Humphris; Angela Chou; Marina Pajic; Christopher J Scarlett; Andreia V Pinho; Marc Giry-Laterriere; Ilse Rooman; Jaswinder S Samra; James G Kench; Jessica A Lovell; Neil D Merrett; Christopher W Toon; Krishna Epari; Nam Q Nguyen; Andrew Barbour; Nikolajs Zeps; Kim Moran-Jones; Nigel B Jamieson; Janet S Graham; Fraser Duthie; Karin Oien; Jane Hair; Robert Grützmann; Anirban Maitra; Christine A Iacobuzio-Donahue; Christopher L Wolfgang; Richard A Morgan; Rita T Lawlor; Vincenzo Corbo; Claudio Bassi; Borislav Rusev; Paola Capelli; Roberto Salvia; Giampaolo Tortora; Debabrata Mukhopadhyay; Gloria M Petersen; Donna M Munzy; William E Fisher; Saadia A Karim; James R Eshleman; Ralph H Hruban; Christian Pilarsky; Jennifer P Morton; Owen J Sansom; Aldo Scarpa; Elizabeth A Musgrove; Ulla-Maja Hagbo Bailey; Oliver Hofmann; Robert L Sutherland; David A Wheeler; Anthony J Gill; Richard A Gibbs; John V Pearson; Nicola Waddell; Andrew V Biankin; Sean M Grimmond
Journal:  Nature       Date:  2016-02-24       Impact factor: 49.962

2.  Genetic Interaction Network Interpretation: A Tidy Data Science Perspective.

Authors:  Lulu Jiang; Hai Fang
Journal:  Methods Mol Biol       Date:  2021

3.  Weighted gene co-expression network analysis of gene modules for the prognosis of esophageal cancer.

Authors:  Cong Zhang; Qian Sun
Journal:  J Huazhong Univ Sci Technolog Med Sci       Date:  2017-06-06

4.  A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery.

Authors:  Teemu J Rintala; Antonio Federico; Leena Latonen; Dario Greco; Vittorio Fortino
Journal:  Brief Bioinform       Date:  2021-11-05       Impact factor: 11.622

5.  Tubular Dickkopf-3 promotes the development of renal atrophy and fibrosis.

Authors:  Giuseppina Federico; Michael Meister; Daniel Mathow; Gunnar H Heine; Gerhard Moldenhauer; Zoran V Popovic; Viola Nordström; Annette Kopp-Schneider; Thomas Hielscher; Peter J Nelson; Franz Schaefer; Stefan Porubsky; Danilo Fliser; Bernd Arnold; Hermann-Josef Gröne
Journal:  JCI Insight       Date:  2016-01-21

6.  Pathway analysis of genomic pathology tests for prognostic cancer subtyping.

Authors:  Olga Lyudovyk; Yufeng Shen; Nicholas P Tatonetti; Susan J Hsiao; Mahesh M Mansukhani; Chunhua Weng
Journal:  J Biomed Inform       Date:  2019-09-06       Impact factor: 6.317

7.  Exploring Transcription Factors-microRNAs Co-regulation Networks in Schizophrenia.

Authors:  Yong Xu; Weihua Yue; Yin Yao Shugart; Sheng Li; Lei Cai; Qiang Li; Zaohuo Cheng; Guoqiang Wang; Zhenhe Zhou; Chunhui Jin; Jianmin Yuan; Lin Tian; Jun Wang; Kai Zhang; Kerang Zhang; Sha Liu; Yuqing Song; Fuquan Zhang
Journal:  Schizophr Bull       Date:  2015-11-24       Impact factor: 9.306

8.  A genetics-led approach defines the drug target landscape of 30 immune-related traits.

Authors:  Hai Fang; Hans De Wolf; Bogdan Knezevic; Katie L Burnham; Julie Osgood; Anna Sanniti; Alicia Lledó Lara; Silva Kasela; Stephane De Cesco; Jörg K Wegner; Lahiru Handunnetthi; Fiona E McCann; Liye Chen; Takuya Sekine; Paul E Brennan; Brian D Marsden; David Damerell; Chris A O'Callaghan; Chas Bountra; Paul Bowness; Yvonne Sundström; Lili Milani; Louise Berg; Hinrich W Göhlmann; Pieter J Peeters; Benjamin P Fairfax; Michael Sundström; Julian C Knight
Journal:  Nat Genet       Date:  2019-06-28       Impact factor: 38.330

9.  Novel phenotype-disease matching tool for rare genetic diseases.

Authors:  Jing Chen; Huan Xu; Anil Jegga; Kejian Zhang; Pete S White; Ge Zhang
Journal:  Genet Med       Date:  2018-06-12       Impact factor: 8.822

10.  Targeting DNA Damage Response and Replication Stress in Pancreatic Cancer.

Authors:  Stephan B Dreyer; Rosie Upstill-Goddard; Viola Paulus-Hock; Clara Paris; Eirini-Maria Lampraki; Eloise Dray; Bryan Serrels; Giuseppina Caligiuri; Selma Rebus; Dennis Plenker; Zachary Galluzzo; Holly Brunton; Richard Cunningham; Mathias Tesson; Craig Nourse; Ulla-Maja Bailey; Marc Jones; Kim Moran-Jones; Derek W Wright; Fraser Duthie; Karin Oien; Lisa Evers; Colin J McKay; Grant A McGregor; Aditi Gulati; Rachel Brough; Ilirjana Bajrami; Stephan Pettitt; Michele L Dziubinski; Juliana Candido; Frances Balkwill; Simon T Barry; Robert Grützmann; Lola Rahib; Amber Johns; Marina Pajic; Fieke E M Froeling; Phillip Beer; Elizabeth A Musgrove; Gloria M Petersen; Alan Ashworth; Margaret C Frame; Howard C Crawford; Diane M Simeone; Chris Lord; Debabrata Mukhopadhyay; Christian Pilarsky; David A Tuveson; Susanna L Cooke; Nigel B Jamieson; Jennifer P Morton; Owen J Sansom; Peter J Bailey; Andrew V Biankin; David K Chang
Journal:  Gastroenterology       Date:  2020-10-09       Impact factor: 22.682

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