Evidence map›Paper›PMID 38800827›Full record

ArticleNAR genomics and bioinformatics2024

PitViper: a software for comparative meta-analysis and annotation of functional screening data.

Paul-Arthur Meslin, Lois M Kelly, Salima Benbarche, Séverine Lecourt, Kevin H Lin, Justine C Rutter, Christopher F Bassil, Raphael Itzykson, Kris C Wood, Alexandre Puissant and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in NAR genomics and bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. 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

11 authors.

Paul-Arthur MeslinUniversité de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.
Lois M KellyUniversité de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.
Salima BenbarcheUniversité de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.
Séverine LecourtUniversité de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.
Kevin H LinDepartment of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
Justine C RutterDepartment of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
Christopher F BassilDepartment of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
Raphael ItzyksonUniversité de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.
Kris C WoodDepartment of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
Alexandre PuissantUniversité de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.
Camille LobryUniversité de Paris Cité, Inserm U944 and CNRS UMR 7212, Institut de Recherche Saint Louis, Hôpital Saint Louis, APHP, 75010 Paris, France.ORCID https://orcid.org/0000-0003-0550-4921

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Recent advancements in shRNA and Cas protein technologies have enabled functional screening methods targeting genes or non-coding regions using single or pooled shRNA and sgRNA. CRISPR-based systems have also been developed for modulating DNA accessibility, resulting in CRISPR-mediated interference (CRISPRi) or activation (CRISPRa) of targeted genes or genomic DNA elements. However, there is still a lack of software tools for integrating diverse array of functional genomics screening outputs that could offer a cohesive framework for comprehensive data integration. Here, we developed PitViper, a flexible and interactive open-source software designed to fill this gap, providing reliable results for the type of elements being screened. It is an end-to-end automated and reproducible bioinformatics pipeline integrating gold-standard methods for functional screening analysis. Our sensitivity analyses demonstrate that PitViper is a useful tool for identifying potential super-enhancer liabilities in a leukemia cell line through genome-wide CRISPRi-based screening. It offers a robust, flexible, and interactive solution for integrating data analysis and reanalysis from functional screening methods, making it a valuable resource for researchers in the field.

Identifiers

PMID38800827
PMCPMC11127635

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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.