Consensus Pathways Implicated in Prognosis of Colorectal Cancer Identified Through Systematic Enrichment Analysis of Gene Expression Profiling Studies

被引:27
|
作者
Lascorz, Jesus [1 ]
Chen, Bowang [1 ]
Hemminki, Kari [1 ,2 ]
Forsti, Asta [1 ,2 ]
机构
[1] German Canc Res Ctr, Div Mol Genet Epidemiol, Heidelberg, Germany
[2] Lund Univ, Ctr Primary Hlth Care Res, Clin Res Ctr, Malmo, Sweden
来源
PLOS ONE | 2011年 / 6卷 / 04期
关键词
II COLON-CANCER; LYMPH-NODE METASTASIS; THERAPEUTIC OPPORTUNITIES; NONNEOPLASTIC MUCOSA; PREDICTS RECURRENCE; LIVER METASTASIS; SIGNATURE; PROGRESSION; GENOME; METAANALYSIS;
D O I
10.1371/journal.pone.0018867
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background: A large number of gene expression profiling (GEP) studies on prognosis of colorectal cancer (CRC) has been performed, but no reliable gene signature for prediction of CRC prognosis has been found. Bioinformatic enrichment tools are a powerful approach to identify biological processes in high-throughput data analysis. Principal Findings: We have for the first time collected the results from the 23 so far published independent GEP studies on CRC prognosis. In these 23 studies, 1475 unique, mapped genes were identified, from which 124 (8.4%) were reported in at least two studies, with 54 of them showing consisting direction in expression change between the single studies. Using these data, we attempted to overcome the lack of reproducibility observed in the genes reported in individual GEP studies by carrying out a pathway-based enrichment analysis. We used up to ten tools for overrepresentation analysis of Gene Ontology (GO) categories or Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in each of the three gene lists (1475, 124 and 54 genes). This strategy, based on testing multiple tools, allowed us to identify the oxidative phosphorylation chain and the extracellular matrix receptor interaction categories, as well as a general category related to cell proliferation and apoptosis, as the only significantly and consistently overrepresented pathways in the three gene lists, which were reported by several enrichment tools. Conclusions: Our pathway-based enrichment analysis of 23 independent gene expression profiling studies on prognosis of CRC identified significantly and consistently overrepresented prognostic categories for CRC. These overrepresented categories have been functionally clearly related with cancer progression, and deserve further investigation.
引用
收藏
页数:9
相关论文
共 50 条
  • [21] GENE-EXPRESSION PROFILE OF THE NORMAL MUCOSA OF PATIENTS WITH COLORECTAL CANCER AND OF NORMAL CONTROLS IDENTIFIED BY GENE MICROARRAY ANALYSIS
    Franceschi, F.
    Fini, L.
    Manno, A.
    Carloni, E.
    Zocco, M. A.
    Di Caro, S.
    Picciocchi, A.
    Coco, C.
    Gasbarrini, G.
    Gasbarrini, A.
    ANNALS OF ONCOLOGY, 2004, 15 : 49 - 49
  • [22] Gene Expression Data Analysis Leads to Better Characterization of Pathways Which Are Involved in Colorectal Cancer
    Shabani, Samira
    BIOMEDICAL AND BIOTECHNOLOGY RESEARCH JOURNAL, 2024, 8 : S27 - S27
  • [23] Bioinformatics analysis of FOLR1 expression, functional enrichment, related signaling pathways and relationship with prognosis in ovarian cancer
    Wang, Yan
    Li, Xiao
    Qu, Pengpeng
    PTERIDINES, 2020, 31 (01) : 46 - 54
  • [24] Novel Drug Candidates for the Treatment of Metastatic Colorectal Cancer through Global Inverse Gene-Expression Profiling
    van Noort, Vera
    Schoelch, Sebastian
    Iskar, Murat
    Zeller, Georg
    Ostertag, Kristina
    Schweitzer, Christine
    Werner, Kristin
    Weitz, Juergen
    Koch, Moritz
    Bork, Peer
    CANCER RESEARCH, 2014, 74 (20) : 5690 - 5699
  • [25] EEPD1 is identified as a predictor of prognosis and immune microenvironment through pan-cancer analysis and related to progression of colorectal cancer
    Guo, Yang
    Li, Shujin
    Shi, Zhan
    Chen, Bingchen
    Wan, Ziang
    Yu, Peng
    Zheng, Boan
    Gong, Wenjing
    Chai, Rui
    Tu, Shiliang
    Yuan, Hang
    HELIYON, 2024, 10 (07)
  • [26] Data supporting the identification of compound for inhibition of survivin of colorectal cancer by using ingenuity pathway analysis of gene expression profiling of colorectal cancer tissues
    Lee, Yi-Chao
    Lee, Jun-Wei
    Huang, Chi-Chen
    Wu, Ming-Heng
    Lee, Kuen-Haur
    DATA IN BRIEF, 2015, 4 : 235 - 238
  • [27] A Meta-Analysis of Gene Expression Profiling Studies Identifies Clinically Relevant Oncogenic Pathways in Basal-Like Breast Cancer.
    Ignatiadis, M.
    Bedard, P. L.
    Haibe-Kains, B.
    Singhal, S. K.
    Loi, S.
    Criscitiello, C.
    Desmedt, C.
    Bontempi, G.
    Piccart, M. J.
    Sotiriou, C.
    CANCER RESEARCH, 2009, 69 (24) : 508S - 508S
  • [28] Genome-Wide Analysis of mRNA Expression Profiling Identified Lung Cancer-Related Gene in Xuanwei, China
    Wu, Chunyan
    Song, Guibo
    Xiong, Guosheng
    Lu, Lingjiao
    Zhou, Xin
    Duan, Yong
    CLINICAL LABORATORY, 2018, 64 (09) : 1517 - 1526
  • [29] Hematopoietic Gene Expression Regulation Through m6A Methylation Predicts Prognosis in Stage III Colorectal Cancer
    Zhou, Zheng
    Mo, Shaobo
    Gu, Ruiqi
    Dai, Weixing
    Zou, Xinhui
    Han, Lingyu
    Zhang, Long
    Wang, Renjie
    Cai, Guoxiang
    FRONTIERS IN ONCOLOGY, 2020, 10
  • [30] Overexpression of TICRR and PPIF confer poor prognosis in endometrial cancer identified by gene co-expression network analysis
    Yang, Linlin
    Cui, Yunxia
    Sun, Xiao
    Wang, Yudong
    AGING-US, 2021, 13 (03): : 4564 - 4589