ArticlePeerJ2013
BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways.
Article in PeerJ, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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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
9 citing papers in PubMed.
- Phase 1 trial of durvalumab (anti-PD-L1) combined with lenalidomide in relapsed/refractory cutaneous T-cell lymphoma.Blood advances · 2025Trial
- Critical Differential Expression Assessment for Individual Bulk RNA-Seq Projects.bioRxiv : the preprint server for biology · 2024Article
- Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps.NPJ systems biology and applications · 2022Article
- Stonewall prevents expression of ectopic genes in the ovary and accumulates at insulator elements in D. melanogaster.PLoS genetics · 2022Article
- Temperature modulates immune gene expression in mosquitoes during arbovirus infection.Open biology · 2021Article
- Pioglitazone-mediated reversal of elevated glucose metabolism in the airway epithelium of mouse lung adenocarcinomas.JCI insight · 2017Article
- A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data.BMC genomics · 2016Article
- Correlation of clinical features and genetic profiles of stromal interaction molecule 1 (STIM1) in colorectal cancers.Oncotarget · 2015Article
- The pathway not taken: understanding 'omics data in the perinatal context.American journal of obstetrics and gynecology · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
BD-Func (BiDirectional FUNCtional enrichment) is an algorithm that calculates functional enrichment by comparing lists of pre-defined genes that are known to be activated versus inhibited in a pathway or by a regulatory molecule. This paper shows that BD-Func can correctly predict cell line alternations and patient characteristics with accuracy comparable to popular algorithms, with a significantly faster run-time. BD-Func can compare scores for individual samples across multiple groups as well as provide predictive statistics and receiver operating characteristic (ROC) plots to quantify the accuracy of the signature associated with a binary phenotypic variable. BD-Func facilitates collaboration and reproducibility by encouraging users to share novel molecular signatures in the BD-Func discussion group, which is where the novel progesterone receptor and LBH589 signatures from this paper can be found. The novel LBH589 signature presented in this paper also serves as a case study showing how a custom signature using cell line data can accurately predict activity in vivo. This software is available to download at https://sourceforge.net/projects/bdfunc/.
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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.