Evidence map›Paper›PMID 39068371›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Incorporating Sequence-Dependent DNA Shape and Dynamics into Transcriptome Data Analysis.

Manisha Kalsan, Almas Jabeen, Shandar Ahmad

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. 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
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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

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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.

Manisha KalsanSchool of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
Almas JabeenSchool of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
Shandar AhmadSchool of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India. shandar@jnu.ac.in.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Differentially expressed genes in a cellular context may be co-regulated by the same transcription factor. However, in the absence of a concurrent transcription factor binding data, such interactions are difficult to detect, especially at the single cell expression level. Motif enrichments in such genes can be used to gain insight into differential expressions caused by the shared upstream TFs. However, it is now established that many genes are co-regulated by the same TF due to a shared DNA shape or sequence-dependent conformational dynamics instead of sequence motif. In this work, we demonstrate how, starting from a gene expression data, such DNA shape and dynamics signatures can be potentially detected using publicly available tools, including DynaSeq, developed in our group for predicting the sequence-dependent components of these DNA shape features.

Indexed as

DNANucleic Acid ConformationComputational BiologyGene Expression ProfilingHumansSoftwareTranscription FactorsTranscriptomeDNATranscription FactorsDNA conformational dynamicsDNA shapeGene expressionSequence motifsTranscription factor

Identifiers

PMID39068371

What OpenQuestion holds

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Read underepoch 390

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.