Evidence map›Paper›PMID 34902127›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2022

Pathway Enrichment Analysis of Microarray Data.

Chiara Pastrello, Yun Niu, Igor Jurisica

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2022. 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. Pathway Analysis Interpretation in the Multi-Omic Era.Biotech (Basel (Switzerland)) · 2025
    Review
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.

Chiara PastrelloOsteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.
Yun NiuOsteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.
Igor JurisicaOsteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada. juris@ai.utoronto.ca.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Microarray analyses usually result in a list of differential genes that need to be annotated to link them the phenotype being studied, help planning validation experiments and interpretation of the results. Pathway enrichment analyses are frequently used for such purpose, where pathways are human created models of molecular activities and processes. While different types of pathway enrichment are available, we focus this protocol on the most frequent type-overrepresentation analysis. Many databases collect different sets of pathways and curate different sets of genes for the same pathways, so it is important to carefully choose the most suitable pathway source to perform enrichment analysis. To provide a comprehensive pathway analysis, in this protocol we will use pathDIP, which supports comprehensive enrichment analysis by integrating 22 main pathway databases. We will also describe the steps needed to visualize the enriched pathways using GSOAP.

Indexed as

Microarray AnalysisComputational BiologyDatabases, FactualGene Expression ProfilingHumansDatabase coverageDatabase overlapEnrichment visualizationPathway consolidationPathway enrichment analysisPathway orphans

Identifiers

PMID34902127

What Socratic 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 Socratic graph.