Evidence map›Paper›PMID 24897108›Full record

ArticlePloS one2014

Integrative analysis of transcriptional regulatory network and copy number variation in intrahepatic cholangiocarcinoma.

Ling Li, Baofeng Lian, Chao Li, Wei Li, Jing Li, Yuannv Zhang, Xianghuo He, Yixue Li, Lu Xie

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed, 1 pooled it
0.7field-weighted citation impact, top 25% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

5 citing papers in PubMed, 1 synthesis or guideline pooled it, 8 citations in OpenAlex.

  1. Meta-analysis of gene expression profiles identifies differential biomarkers for hepatocellular carcinoma and cholangiocarcinoma.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2016
    Pooled it
  2. Article
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  4. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 5 institutions in 1 country.

Ling LiSchool of Life Sciences and Technology, Tongji University, Shanghai, P.R.China; Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China.
Baofeng LianShanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China; School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China.
Chao LiKey Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China.
Wei LiShanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China.
Jing LiShanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China.
Yuannv ZhangKey Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China.
Xianghuo HeKey Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China.
Yixue LiSchool of Life Sciences and Technology, Tongji University, Shanghai, P.R.China; School of Life Sciences and Technology, Shanghai Jiaotong University, Shanghai, P.R.China; Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R.China.
Lu XieShanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, P.R.China.
Shanghai Center For Bioinformation Technology · CNShanghai Academy of Science & Technology · CNShanghai Institutes for Biological Sciences · CNChinese Academy of Sciences · CNTongji University · CN

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundTranscriptional regulatory network (TRN) is used to study conditional regulatory relationships between transcriptional factors and genes. However few studies have tried to integrate genomic variation information such as copy number variation (CNV) with TRN to find causal disturbances in a network. Intrahepatic cholangiocarcinoma (ICC) is the second most common hepatic carcinoma with high malignancy and poor prognosis. Research about ICC is relatively limited comparing to hepatocellular carcinoma, and there are no approved gene therapeutic targets yet.

methodWe first constructed TRN of ICC (ICC-TRN) using forward-and-reverse combined engineering method, and then integrated copy number variation information with ICC-TRN to select CNV-related modules and constructed CNV-ICC-TRN. We also integrated CNV-ICC-TRN with KEGG signaling pathways to investigate how CNV genes disturb signaling pathways. At last, unsupervised clustering method was applied to classify samples into distinct classes.

resultWe obtained CNV-ICC-TRN containing 33 modules which were enriched in ICC-related signaling pathways. Integrated analysis of the regulatory network and signaling pathways illustrated that CNV might interrupt signaling through locating on either genomic sites of nodes or regulators of nodes in a signaling pathway. In the end, expression profiles of nodes in CNV-ICC-TRN were used to cluster the ICC patients into two robust groups with distinct biological function features.

conclusionOur work represents a primary effort to construct TRN in ICC, also a primary effort to try to identify key transcriptional modules based on their involvement of genetic variations shown by gene copy number variations (CNV). This kind of approach may bring the traditional studies of TRN based only on expression data one step further to genetic disturbance. Such kind of approach can easily be extended to other disease samples with appropriate data.

Indexed as

DNA Copy Number VariationsGene Regulatory NetworksBile Duct NeoplasmsBile Ducts, IntrahepaticCholangiocarcinomaChromosome AberrationsCluster AnalysisComputational BiologyDatabases, Nucleic AcidGene Expression ProfilingGene Expression Regulation, NeoplasticHumansMAP Kinase Signaling SystemSignal TransductionTransforming Growth Factor betaWnt Signaling PathwayTransforming Growth Factor beta

Identifiers

PMID24897108
PMCPMC4045758
OpenAlexW1996615395

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.