A novel DNA sequence motif in human and mouse genomes.

Shilu Zhang, Fang Du, Hongkai Ji

Abstract read

In one paragraph

Article in Scientific reports, 2015. 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

3 authors.

Shilu ZhangDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA.

Fang DuDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA.

Hongkai JiDepartment of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, Maryland 21205, USA.

Funding

Statistical and Computational Tools for Next-generation ChIP-seq ApplicationsR01HG006841 · NHGRI · JOHNS HOPKINS UNIVERSITY · PI JI, HONGKAI · 2012 to 2014

$951k

NHGRI NIH HHS R01 HG006841NHGRI NIH HHS R01HG006841

6 · The paper itself

Abstract

We report a novel DNA sequence motif in human and mouse genomes. This motif has several interesting features indicating that it is highly likely to be an unknown functional sequence element. The motif is highly enriched in promoter regions. Locations of the motif sites in the genome have strong tendency to be clustered together. Motif sites are associated with increased phylogenetic conservation as well as elevated DNase I hypersensitivity (DHS) in ENCODE cell lines. Clustered motif sites are found in promoter regions of a substantial fraction of the protein-coding genes in the genome. All together, these indicate that the motif may have important functions associated with a large number of genes.

Indexed as

AnimalsBase SequenceBinding SitesChromatin ImmunoprecipitationConserved SequenceDeoxyribonuclease IDNAGenomeHumansKruppel-Like Transcription FactorsMiceNerve Tissue ProteinsNucleotide MotifsPhylogenyPromoter Regions, GeneticZinc Finger Protein Gli3Deoxyribonuclease IDNAGli3 protein, mouseKruppel-Like Transcription FactorsNerve Tissue ProteinsZinc Finger Protein Gli3

Identifiers

PMID25990515

DOI10.1038/srep10444

PMCPMC4438489

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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.