ArticleBioinformatics (Oxford, England)2015
Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 1 of them a synthesis that pooled 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.
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.
Who cites it
11 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Transcriptomics and network analysis highlight potential pathways in the pathogenesis of pterygium.Scientific reports · 2022Pooled it
- Complex I inhibitor of oxidative phosphorylation in advanced solid tumors and acute myeloid leukemia: phase I trials.Nature medicine · 2023Article
- Article
- Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing.Frontiers in genetics · 2020Article
- CisPi: a transcriptomic score for disclosing cis-acting disease-associated lincRNAs.Bioinformatics (Oxford, England) · 2018Article
- Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm.eLife · 2017Article
- Incorporating genomic, transcriptomic and clinical data: a prognostic and stem cell-like MYC and PRC imbalance in high-risk neuroblastoma.BMC systems biology · 2017Article
- A c-Myc-regulated stem cell-like signature in high-risk neuroblastoma: A systematic discovery (Target neuroblastoma ESC-like signature).Scientific reports · 2017Article
- High Throughput Sequencing for Detection of Foodborne Pathogens.Frontiers in microbiology · 2017Review
- RGmatch: matching genomic regions to proximal genes in omics data integration.BMC bioinformatics · 2016Article
- Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks.Nature communications · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
unlabelledSeq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci, adapted for advances in genome research. Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores. It is designed to isolate systematic disturbances and common biological underpinnings from next-generation sequencing (NGS) data. Seq2pathway offers Bioconductor users enhanced capability in discovering collective pathway effects caused by both coding genes and cis-regulation of non-coding elements. AVAILABILITY AND IMPLEMENTATION: The package is freely available at http://www.bioconductor.org/packages/release/bioc/html/seq2pathway.html. CONTACT: xyang2@uchicago.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.