Evidence map›Paper›PMID 33961216›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2021

Comparative Analysis of Core and Accessory Genes in Coexpression Network.

Biliang Zhang, Jian Jiao, Pan Zhang, Wen-Jing Cui, Ziding Zhang, Chang-Fu Tian

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Review
  3. 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.

Biliang ZhangState Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.
Jian JiaoState Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.
Pan ZhangState Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.
Wen-Jing CuiState Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.
Ziding ZhangState Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China.
Chang-Fu TianState Key Laboratory of Agrobiotechnology, and College of Biological Sciences, China Agricultural University, Beijing, China. cftian@cau.edu.cn.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Prokaryotes harbor a various proportion of accessory genes in their genomes. The integration of accessory functions with the core regulation network is critical for environmental adaptation, particularly considering a theoretically unlimited number of niches on the earth for microorganisms. Comparative genomics can reveal a co-occurrence pattern between a subset of accessory genes (or variations in core genes) and an adaptation trait, while comparative transcriptomics can further uncover whether a coordinated regulation of gene expression is involved. In this chapter, we introduce a protocol for weighted gene coexpression network construction by using well-developed open source tools, and a further application of such a network in comparative analysis of bacterial core and accessory genes.

Indexed as

Gene Regulatory NetworksGenome, BacterialGenomicsDatabases, GeneticDNA, BacterialGene Expression Regulation, BacterialPhylogenyResearch DesignSinorhizobium frediiWorkflowDNA, BacterialAccessory geneCoexpressionCore geneNetwork analysisOrthologsWGCNA

Identifiers

PMID33961216

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.