Evidence map›Paper›PMID 37249891›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

Differential Expression Feature Extraction (DEFE): A Case Study in Wheat FHB RNA-Seq Data Analysis.

Youlian Pan, Anuradha Surendra, Ziying Liu, Thérèse Ouellet, Nora A Foroud

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. 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

5 authors.

Youlian PanDigital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada. Youlian.Pan@nrc-cnrc.gc.ca.
Anuradha SurendraDigital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada.
Ziying LiuDigital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada.
Thérèse OuelletOttawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada.
Nora A ForoudLethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset in order to detect the association between such a group of genes and an experimental condition. This is often done through a clustering approach, such as k-means or bipartition hierarchical clustering, based on particular similarity measures in the grouping process. In such a dataset, the gene differential expression itself is an innate attribute that can be used in the feature extraction process. For example, in a dataset consisting of multiple treatments versus their controls, the expression of a gene in each treatment would have three possible behaviors, upregulated, downregulated, or unchanged. We present in this chapter, a differential expression feature extraction (DEFE) method by using a string consisting of three numerical values at each character to denote such behavior, i.e., 1 = up, 2 = down, and 0 = unchanged, which results in up to 3

Indexed as

FusariumTriticumPlant DiseasesRNA-SeqBioinformaticsCo-expressionDifferential expression feature extractionDifferential gene expressionFusarium graminearumFusarium head blightGene regulationRNA-seqWheat

Identifiers

PMID37249891

What OpenQuestion holds

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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.