Dataset Information

CIGene: a literature-based online resource for cancer initiation genes.

ABSTRACT:

Background

Cancer initiation genes (CIGs) are genes that can directly promote cell proliferation or induce cancer. There are thousands of published studies identifying various CIGs; however, no systematic collection or description is available.

Results

To construct a CIG reference for genetic screening, we have collected 177 human genes curated from 1507 PubMed abstracts. To facilitate data queries and browsing, the identified CIGs along with extensive bioinformatic annotations were stored in an online database called CIGene. Initial functional analysis revealed an overlooked role for cell motility in cancer initiation. Subsequent cross-referencing of known tumor suppressor genes and oncogenes against the 177 CIGs identified 96 and 81 CIGs with and without known oncogenic roles, respectively. Successive network analyses of all 177 CIGs determined that the two groups of genes were more likely to link within their group. The distinct molecular functions for these groups were also confirmed with functional studies. While the 96 known oncogenic genes had fundamental roles in gene regulation and signaling, the remaining 81 genes possessed more ancillary functions, such enhancer binding. Further network and mutational analysis of the 96 known oncogenic genes revealed that mutations in these genes were highly prevalent in multiple cancers. By focusing on breast cancer, we found that 32 of the 96 genes with mutations in breast cancers were significantly associated with patient survival.

Conclusions

As the first literature-based online resource for CIGs, CIGene will serve as a useful gateway for the systematic analysis of cancer initiation. CIGene is freely available to all academic users at http://soft.bioinfo-minzhao.org/cigene/ .

SUBMITTER: Liu Y

PROVIDER: S-EPMC6060465 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

CIGene: a literature-based online resource for cancer initiation genes.

Liu Yining Y Luo Mingyu M Li Qijun Q Lu Jiachun J Zhao Min M Qu Hong H

BMC genomics 20180725 1

<h4>Background</h4>Cancer initiation genes (CIGs) are genes that can directly promote cell proliferation or induce cancer. There are thousands of published studies identifying various CIGs; however, no systematic collection or description is available.<h4>Results</h4>To construct a CIG reference for genetic screening, we have collected 177 human genes curated from 1507 PubMed abstracts. To facilitate data queries and browsing, the identified CIGs along with extensive bioinformatic annotations we ...[more]

PMID: 30045691

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Project description:The last two decades have witnessed a dramatic acceleration in the production of genomic sequence information and publication of biomedical articles. Despite the fact that genome sequence data and publications are two of the most heavily relied-upon sources of information for many biologists, very little effort has been made to systematically integrate data from genomic sequences directly with the biological literature. For a limited number of model organisms dedicated teams manually curate publications about genes; however for species with no such dedicated staff many thousands of articles are never mapped to genes or genomic regions.To overcome the lack of integration between genomic data and biological literature, we have developed pubmed2ensembl (http://www.pubmed2ensembl.org), an extension to the BioMart system that links over 2,000,000 articles in PubMed to nearly 150,000 genes in Ensembl from 50 species. We use several sources of curated (e.g., Entrez Gene) and automatically generated (e.g., gene names extracted through text-mining on MEDLINE records) sources of gene-publication links, allowing users to filter and combine different data sources to suit their individual needs for information extraction and biological discovery. In addition to extending the Ensembl BioMart database to include published information on genes, we also implemented a scripting language for automated BioMart construction and a novel BioMart interface that allows text-based queries to be performed against PubMed and PubMed Central documents in conjunction with constraints on genomic features. Finally, we illustrate the potential of pubmed2ensembl through typical use cases that involve integrated queries across the biomedical literature and genomic data.By allowing biologists to find the relevant literature on specific genomic regions or sets of functionally related genes more easily, pubmed2ensembl offers a much-needed genome informatics inspired solution to accessing the ever-increasing biomedical literature.

Project description:BackgroundRecruiting the target number of participants within the pre-specified time frame agreed with funders remains a common challenge in the completion of a successful clinical trial and addressing this is an important methodological priority. While there is growing research around recruitment, navigating this literature to support an evidence-based approach remains difficult. The Online resource for Recruitment Research in Clinical triAls project aims to create an online searchable database of recruitment research to improve access to existing evidence and to identify gaps for future research.MethodsMEDLINE (Ovid), Scopus, Cochrane Database of Systematic Reviews and Cochrane Methodology Register, Science Citation Index Expanded and Social Sciences Citation Index within the ISI Web of Science and Education Resources Information Center were searched in January 2015. Search strategy results were screened by title and abstract, and full text obtained for potentially eligible articles. Studies reporting or evaluating strategies, interventions or methods used to recruit patients were included along with case reports and studies exploring reasons for patient participation or non-participation. Eligible articles were categorised as systematic reviews, nested randomised controlled trials and other designs evaluating the effects of recruitment strategies (Level 1); studies that report the use of recruitment strategies without an evaluation of impact (Level 2); or articles reporting factors affecting recruitment without presenting a particular recruitment strategy (Level 3). Articles were also assigned to 1, or more, of 42 predefined recruitment domains grouped under 6 categories.ResultsMore than 60,000 records were retrieved by the search, resulting in 56,030 unique titles and abstracts for screening, with a further 23 found through hand searches. A total of 4570 full text articles were checked; 2804 were eligible. Six percent of the included articles evaluated the effectiveness of a recruitment strategy (Level 1), with most of these assessing aspects of participant information, either its method of delivery (33%) or its content and format (28%).DiscussionRecruitment to clinical trials remains a common challenge and an important area for future research. The online resource for Recruitment Research in Clinical triAls project provides a searchable, online database of research relevant to recruitment. The project has identified the need for researchers to evaluate their recruitment strategies to improve the evidence base and broaden the narrow focus of existing research to help meet the complex challenges faced by those recruiting to clinical trials.

Dataset Information

CIGene: a literature-based online resource for cancer initiation genes.

Background

Results

Conclusions

Publications

CIGene: a literature-based online resource for cancer initiation genes.

Similar Datasets

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