Identifying prognostic features by bottom-up approach and correlating to drug repositioning

PloS One
Wei LiLu Xie

Abstract

Traditionally top-down method was used to identify prognostic features in cancer research. That is to say, differentially expressed genes usually in cancer versus normal were identified to see if they possess survival prediction power. The problem is that prognostic features identified from one set of patient samples can rarely be transferred to other datasets. We apply bottom-up approach in this study: survival correlated or clinical stage correlated genes were selected first and prioritized by their network topology additionally, then a small set of features can be used as a prognostic signature. Gene expression profiles of a cohort of 221 hepatocellular carcinoma (HCC) patients were used as a training set, 'bottom-up' approach was applied to discover gene-expression signatures associated with survival in both tumor and adjacent non-tumor tissues, and compared with 'top-down' approach. The results were validated in a second cohort of 82 patients which was used as a testing set. Two sets of gene signatures separately identified in tumor and adjacent non-tumor tissues by bottom-up approach were developed in the training cohort. These two signatures were associated with overall survival times of HCC patients and the robustness o...Continue Reading

References

Sep 10, 1998·Hepatology : Official Journal of the American Association for the Study of Liver Diseases
Oct 13, 1999·Seminars in Liver Disease·J M LlovetJ Bruix
Apr 20, 2001·Proceedings of the National Academy of Sciences of the United States of America·V G TusherG Chu
Feb 2, 2002·Nature·Laura J van 't VeerStephen H Friend
Mar 10, 2004·Proceedings of the National Academy of Sciences of the United States of America·A BarratA Vespignani
Apr 20, 2004·PLoS Biology·Eric Bair, Robert Tibshirani
Jun 8, 2004·The Journal of Clinical Endocrinology and Metabolism·Priya MohantyParesh Dandona
Sep 7, 2004·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Ju-Seog LeeSnorri S Thorgeirsson
Jul 5, 2006·British Journal of Cancer·C C SchimanskiM Moehler
Jul 31, 2007·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Jian-Min YuanMimi C Yu
Nov 17, 2007·Bioinformatics·Yassen AssenovMario Albrecht
Apr 11, 2008·Journal of Gastroenterology and Hepatology·Mimi C YuShelly C Lu
Apr 9, 2008·Journal of Theoretical Biology·Sohyun HwangDoheon Lee
Oct 17, 2008·The New England Journal of Medicine·Yujin HoshidaTodd R Golub
Mar 26, 2010·Automated Experimentation·Karthik Raman
Jun 1, 2010·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Jun YuJoseph J Y Sung
Nov 10, 2010·Nucleic Acids Research·Craig KnoxDavid S Wishart
Oct 14, 2011·The New England Journal of Medicine·Hashem B El-Serag
Nov 23, 2011·Hepatology : Official Journal of the American Association for the Study of Liver Diseases·Soo Mi KimJu-Seog Lee
Dec 15, 2011·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Pauline LagardeFrédéric Chibon
Mar 20, 2012·European Journal of Cancer : Official Journal for European Organization for Research and Treatment of Cancer (EORTC) [and] European Association for Cancer Research (EACR)·UNKNOWN European Association for Study of Liver, UNKNOWN European Organisation for Research and Treatment of Cancer
Mar 20, 2012·Journal of Hepatology·UNKNOWN European Association For The Study Of The Liver, UNKNOWN European Organisation For Research And Treatment Of Cancer
Apr 12, 2012·Nature Biotechnology·Philippe SanseauVincent Mooser
Apr 10, 2013·Gastroenterology·Jean-Charles NaultJessica Zucman-Rossi
May 25, 2013·Journal of Gastroenterology·Takeo ToshimaYoshihiko Maehara
Jun 13, 2013·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Eun Ju ChoHyo-Suk Lee
Jan 1, 2011·Cancers·Carmen BerasainMatías A Avila
Nov 28, 2013·CNS Neuroscience & Therapeutics·Zhao-Shi BaoTao Jiang
Jan 7, 2014·Nature·Yukinori OkadaRobert M Plenge

❮ Previous
Next ❯

Citations

Sep 30, 2015·Scientific Reports·Andrea WeissPatrycja Nowak-Sliwinska
Mar 3, 2020·Frontiers in Genetics·Chunyu WangMaozu Guo
Sep 10, 2020·Frontiers in Bioengineering and Biotechnology·Qingwen LiQingyuan Li
Jun 23, 2020·BioMed Research International·Chao WangShuguang Han

❮ Previous
Next ❯

Methods Mentioned

BETA
CLIP

Software Mentioned

GSEA
Network Analyzer Cytoscape
ProgNGenes
MammaPrint
Linear Models for Microarray Data ( limma )
Cytoscape
LOOCV
ProgGenes
R

Related Concepts

Related Feeds

Carcinoma, Hepatocellular

Hepatocellular Carcinoma is a malignant cancer in liver epithelial cells. Discover the latest research on Hepatocellular Carcinoma here.

Cancer Genomics (Keystone)

Cancer genomics approaches employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Discover the latest research using such technologies in this feed.

Anti-inflammatory Treatments

A drug or substance that reduces inflammation (redness, swelling, and pain) in the body. Anti-inflammatory agents block certain substances in the body that cause inflammation and swelling. Discover the latest research on anti-inflammatory treatments here

Cancer Metabolism

In order for cancer cells to maintain rapid, uncontrolled cell proliferation, they must acquire a source of energy. Cancer cells acquire metabolic energy from their surrounding environment and utilize the host cell nutrients to do so. Here is the latest research on cancer metabolism.

Breast Cancer: Risk Factors

Breast cancer is a multifactorial disease that is influenced by both environmental and genetic factors. Discover the latest research on the environmental and genetic risk factors for breast cancer here.

Breast Invasive Carcinoma (Keystone)

Invasive breast cancers indicate a spread into breast tissues and lymph nodes. Here are the latest discoveries pertaining to breast invasive carcinomas.

Breast Invasive Carcinoma

Invasive breast cancers indicate a spread into breast tissues and lymph nodes. Here are the latest discoveries pertaining to breast invasive carcinomas.