Evidence map›Paper›PMID 35524179›Full record

ArticleBMC genomics2022

Identification of condition-specific regulatory mechanisms in normal and cancerous human lung tissue.

Yuqing Hang, Josh Burns, Benjamin T Shealy, Rini Pauly, Stephen P Ficklin, Frank A Feltus

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

Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.1field-weighted citation impact, top 59% 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

1 citing paper in PubMed, 1 citations in OpenAlex.

  1. Article
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

6 authors at 2 institutions in 1 country.

Yuqing HangDepartment of Genetics & Biochemistry, Clemson University, Clemson, 29634, USA.
Josh BurnsDepartment of Horticulture, Washington State University, Pullman, 99164, USA.
Benjamin T ShealyDepartment of Electrical and Computer Engineering, Clemson University, Clemson, 29634, USA.
Rini PaulyBiomedical Data Science and Informatics Program, Clemson University, Clemson, 29634, USA.
Stephen P FicklinDepartment of Horticulture, Washington State University, Pullman, 99164, USA.
Frank A FeltusDepartment of Genetics & Biochemistry, Clemson University, Clemson, 29634, USA. ffeltus@clemson.edu.
Clemson University · USWashington State University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundLung cancer is the leading cause of cancer death in both men and women. The most common lung cancer subtype is non-small cell lung carcinoma (NSCLC) comprising about 85% of all cases. NSCLC can be further divided into three subtypes: adenocarcinoma (LUAD), squamous cell carcinoma (LUSC), and large cell lung carcinoma. Specific genetic mutations and epigenetic aberrations play an important role in the developmental transition to a specific tumor subtype. The elucidation of normal lung versus lung tumor gene expression patterns and regulatory targets yields biomarker systems that discriminate lung phenotypes (i.e., biomarkers) and provide a foundation for the discovery of normal and aberrant gene regulatory mechanisms.

resultsWe built condition-specific gene co-expression networks (csGCNs) for normal lung, LUAD, and LUSC conditions. Then, we integrated normal lung tissue-specific gene regulatory networks (tsGRNs) to elucidate control-target biomarker systems for normal and cancerous lung tissue. We characterized co-expressed gene edges, possibly under common regulatory control, for relevance in lung cancer.

conclusionsOur approach demonstrates the ability to elucidate csGCN:tsGRN merged biomarker systems based on gene expression correlation and regulation. The biomarker systems we describe can be used to classify and further describe lung specimens. Our approach is generalizable and can be used to discover and interpret complex gene expression patterns for any condition or species.

Indexed as

Adenocarcinoma of LungCarcinoma, Non-Small-Cell LungLung NeoplasmsBiomarkersBiomarkers, TumorFemaleGene Expression Regulation, NeoplasticHumansLungPrognosisBiomarkersBiomarkers, TumorBiomarker systemGene co-expression networkGene regulatory networkLung cancerRegulation

Identifiers

PMID35524179
PMCPMC9077899
OpenAlexW4229072523

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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.