Evidence map›Paper›PMID 29487738›Full record

ArticleF1000Research2017

A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression.

Daniel Carlin, Kassi Kosnicki, Sara Garamszegi, Trey Ideker, Helga Thorvaldsdóttir, Michael Reich, Jill Mesirov

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in F1000Research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

7 authors.

Daniel CarlinThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USA.ORCID https://orcid.org/0000-0001-5075-9486
Kassi KosnickiThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USA.
Sara GaramszegiBroad Institute, Cambridge, MA, 02142, USA.
Trey IdekerThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USA.
Helga ThorvaldsdóttirBroad Institute, Cambridge, MA, 02142, USA.
Michael ReichThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USA.
Jill MesirovThe University of California, San Diego School of Medicine, 500 Gilman Dr, La Jolla, CA, 92093, USA.

Funding

TR&D 3 - Network Guided Machine LearningP41GM103504 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IDEKER, TREY · 2012 to 2024
$17.3M
GenomeSpace: community web environment for analysis across diverse genomic toolsU41HG007517 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2014 to 2017
$7.5M
Supporting Integrative Genomic Analysis Users with GenePatternR01GM074024 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2005 to 2019
$6.6M
GenePattern Notebooks for Cancer ResearchU24CA194107 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2015 to 2019
$2.8M
NCI NIH HHS U24 CA194107NHGRI NIH HHS U41 HG007517NIGMS NIH HHS P41 GM103504NIGMS NIH HHS R01 GM074024
6 · The paper itself

Abstract

One commonly performed bioinformatics task is to infer functional regulation of transcription factors by observing differential expression under a knockout, and integrating DNA binding information of that transcription factor.   However, until now, this task has required dedicated bioinformatics support to perform the necessary data integration. GenomeSpace provides a protocol, or "recipe", and a user interface with inter-operating software tools to identify protein occupancies along the genome from a ChIP-seq experiment and associated differentially regulated genes from a RNA-Seq experiment. By integrating RNA-Seq and ChIP-seq analyses, a user is easily able to associate differing expression phenotypes with changing epigenetic landscapes.

Indexed as

ChIP-seqdata integrationdifferential expressionepigeneticshistone modificationregulationRNA-Seqtranscription factor

Identifiers

PMID29487738
PMCPMC5806050

What OpenQuestion holds

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Registered trials

None linked

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.