Evidence map›Paper›PMID 36865134›Full record

ArticlebioRxiv : the preprint server for biology2023

PANGEA: A New Gene Set Enrichment Tool for

Yanhui Hu, Aram Comjean, Helen Attrill, Giulia Antonazzo, Jim Thurmond, Fangge Li, Tiffany Chao, Stephanie E Mohr, Nicholas H Brown, Norbert Perrimon

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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

5 · Who and what money

Authors and funding

10 authors.

Yanhui HuDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
Aram ComjeanDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
Helen AttrillDepartment of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
Giulia AntonazzoDepartment of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
Jim ThurmondDepartment of Biology, Indiana University, Bloomington, IN 47405, USA.
Fangge LiDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
Tiffany ChaoDrosophila RNAi Screening Center, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
Stephanie E MohrDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.
Nicholas H BrownDepartment of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK.
Norbert PerrimonDepartment of Genetics, Blavatnik Institute, Harvard Medical School, Harvard University, Boston, MA 02115, USA.

Funding

Resource Project CoreU41HG000739 · NHGRI · HARVARD UNIVERSITY · PI PERRIMON, NORBERT · 2014 to 2022
$32.3M
Functional genomics resources for the Drosophila - TR&D3P41GM132087 · NIGMS · HARVARD MEDICAL SCHOOL · PI PERRIMON, NORBERT · 2019 to 2023
$6.8M
Medical Research Council MR/N030117/1Medical Research Council MR/W024233/1NHGRI NIH HHS U41 HG000739NIGMS NIH HHS P41 GM132087
6 · The paper itself

Abstract

Gene set enrichment analysis (GSEA) plays an important role in large-scale data analysis, helping scientists discover the underlying biological patterns over-represented in a gene list resulting from, for example, an 'omics' study. Gene Ontology (GO) annotation is the most frequently used classification mechanism for gene set definition. Here we present a new GSEA tool, PANGEA (PAthway, Network and Gene-set Enrichment Analysis; https://www.flyrnai.org/tools/pangea/ ), developed to allow a more flexible and configurable approach to data analysis using a variety of classification sets. PANGEA allows GO analysis to be performed on different sets of GO annotations, for example excluding high-throughput studies. Beyond GO, gene sets for pathway annotation and protein complex data from various resources as well as expression and disease annotation from the Alliance of Genome Resources (Alliance). In addition, visualisations of results are enhanced by providing an option to view network of gene set to gene relationships. The tool also allows comparison of multiple input gene lists and accompanying visualisation tools for quick and easy comparison. This new tool will facilitate GSEA for

Identifiers

PMID36865134
PMCPMC9980003

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.