Evidence map›Paper›PMID 25428347›Full record

ArticleNucleic acids research2015

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.

Aaron A Diaz, Han Qin, Miguel Ramalho-Santos, Jun S Song

Abstract readValidation Study
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.

0numbers the graph read from it
0cells of the map it votes in
36citing 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

36 citing papers in PubMed.

  1. Potential promising of synthetic lethality in cancer research and treatment.Naunyn-Schmiedeberg's archives of pharmacology · 2025
    Review
  2. Review
  3. The Current Situation and Development Prospect of Whole-Genome Screening.International journal of molecular sciences · 2024
    Review
  4. Article
  5. Review
  6. Computational Tools and Resources for CRISPR/Cas Genome Editing.Genomics, proteomics & bioinformatics · 2023
    Review
  7. Article
  8. Article
  9. Review
  10. Common computational tools for analyzing CRISPR screens.Emerging topics in life sciences · 2021
    Review
  11. Review
  12. Article
  13. Article
  14. Review
  15. Article
  16. Review
  17. Review
  18. Review
  19. Article
  20. Frontiers in oncology · 2020
    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

4 authors.

Aaron A DiazInstitute for Human Genetics, University of California, San Francisco, CA, USA The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA.
Han QinThe Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Departments of Obstetrics and Gynecology and Pathology and Center for Reproductive Sciences, University of California, San Francisco, CA, USA Diabetes Center, University of California, San Francisco, CA, USA.
Miguel Ramalho-SantosThe Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Departments of Obstetrics and Gynecology and Pathology and Center for Reproductive Sciences, University of California, San Francisco, CA, USA Diabetes Center, University of California, San Francisco, CA, USA songj@illinois.edu.
Jun S SongInstitute for Human Genetics, University of California, San Francisco, CA, USA The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA songj@illinois.edu.

Funding

Predicting Transcriptional and Epigenetic Networks in Cancer from Sequencing DataR01CA163336 · NCI · UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN · PI Jun S Song · 2012 to 2026
$4.4M
Role of pluripotency in development of the germlineDP2OD004698 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI RAMALHO-SANTOS, MIGUEL · 2008 to 2008
$2.3M
NCI NIH HHS R01 CA163336NCI NIH HHS R01CA163336NIH HHS DP2OD4698
6 · The paper itself

Abstract

Genetic screens of an unprecedented scale have recently been made possible by the availability of high-complexity libraries of synthetic oligonucleotides designed to mediate either gene knockdown or gene knockout, coupled with next-generation sequencing. However, several sources of random noise and statistical biases complicate the interpretation of the resulting high-throughput data. We developed HiTSelect, a comprehensive analysis pipeline for rigorously selecting screen hits and identifying functionally relevant genes and pathways by addressing off-target effects, controlling for variance in both gene silencing efficiency and sequencing depth of coverage and integrating relevant metadata. We document the superior performance of HiTSelect using data from both genome-wide RNAi and CRISPR/Cas9 screens. HiTSelect is implemented as an open-source package, with a user-friendly interface for data visualization and pathway exploration. Binary executables are available at http://sourceforge.net/projects/hitselect/, and the source code is available at https://github.com/diazlab/HiTSelect.

Indexed as

High-Throughput Nucleotide SequencingAlgorithmsClustered Regularly Interspaced Short Palindromic RepeatsGene Knockdown TechniquesInduced Pluripotent Stem CellsNeoplastic Stem CellsRNAStochastic ProcessesRNA

Identifiers

PMID25428347
PMCPMC4330337

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.