ArticleBMC bioinformatics2018
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,083 papers.
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
1,083 citing papers in PubMed, 1,671 citations in OpenAlex.
- Transauricular Vagus Nerve Stimulation in Acute Ischaemic Stroke Requiring Mechanical Thrombectomy: Sham-Controlled, Randomised Device Trial.Translational stroke research · 2025Trial
- Host andGut microbes · 2026Article
- Bacterial constipation: Mucin-degrading intestinal commensal bacteria cause constipation.Gut microbes · 2026Article
- Store-operated calcium signaling modulators improve a dendritic cell-based vaccine against melanoma.Oncoimmunology · 2026Article
- Helios is critical for Treg effector differentiation in adipose autoimmunity.The Journal of experimental medicine · 2026Article
- Reactivation of a loss-of-function SlGLK2 allele by frame-restoring genome editing in tomato.Plant cell reports · 2026Article
- PBMC-derived RNA signatures show impaired ability to regulate immune responses in women developing preeclampsia†.Biology of reproduction · 2026Article
- In vivo screen for osteoclast derived osteogenic factors using non-resorptive osteoclasts in zebrafish bone.G3 (Bethesda, Md.) · 2026Article
- Unique circulating miRNAome signatures captured with distinct molecular states in Lynch syndrome and sporadic colorectal cancer.Molecular oncology · 2026Article
- Detergent-Containing Toothpaste Decreases Esophageal Mucosal Impedance and Alters Salivary Properties in Humans.Allergy · 2026Article
- Leptin May Promote Eosinophilic CRSwNP Progression by Enhancing Eosinophil Chemotaxis and Angiogenesis Under a Type 2 Inflammatory Milieu.International forum of allergy & rhinology · 2026Article
- Role of the tomato MARS1/ROUGH gene encoding a LYSINE-SPECIFIC HISTONE DEMETHYLASE 1 in adventitious root and fruit skin formation.Journal of integrative plant biology · 2026Article
- Canine Distemper Virus-Induced Transcriptional Modulation of Canine Histiocytic Sarcoma Cells in an In Vitro Model of Tumour Zones.Journal of cellular and molecular medicine · 2026Article
- Root-sourced 1-aminocyclopropane-1-carboxylic acid modulates development and adaptive responses to salinity in tomato.The Plant journal : for cell and molecular biology · 2026Article
- The histone methyltransferase complex subunit RBBP5 serves as a central epigenetic regulator of proteostasis dynamics.PLoS biology · 2026Article
- Cannabidiol (CBD) differentially shapes systemic cytokines and transcriptomic profiles in the liver and spleen: insights from a male mouse model.Molecular genetics and genomics : MGG · 2026Article
- Targeting the ERK Signaling Pathway to Halt Adventitia Remodeling of Ascending Thoracic Aortic Aneurysm.JACC. Basic to translational science · 2026Article
- Establishment of Patient-Derived Xenotransplant and Cell Line Models for Canine B-Cell Lymphoma.Cells · 2026Article
- High-resolution CRISPR/Cas9 screens identify PAK2 as a suppressor of macrophage proliferation.bioRxiv : the preprint server for biology · 2026Article
- Injury polarized CD4Redox biology · 2026Article
1,023 more citing papers are in PubMed but not listed here.
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 at 1 institution in 1 country.
Funding
Abstract
backgroundRNA-seq is widely used for transcriptomic profiling, but the bioinformatics analysis of resultant data can be time-consuming and challenging, especially for biologists. We aim to streamline the bioinformatic analyses of gene-level data by developing a user-friendly, interactive web application for exploratory data analysis, differential expression, and pathway analysis.
resultsiDEP (integrated Differential Expression and Pathway analysis) seamlessly connects 63 R/Bioconductor packages, 2 web services, and comprehensive annotation and pathway databases for 220 plant and animal species. The workflow can be reproduced by downloading customized R code and related pathway files. As an example, we analyzed an RNA-Seq dataset of lung fibroblasts with Hoxa1 knockdown and revealed the possible roles of SP1 and E2F1 and their target genes, including microRNAs, in blocking G1/S transition. In another example, our analysis shows that in mouse B cells without functional p53, ionizing radiation activates the MYC pathway and its downstream genes involved in cell proliferation, ribosome biogenesis, and non-coding RNA metabolism. In wildtype B cells, radiation induces p53-mediated apoptosis and DNA repair while suppressing the target genes of MYC and E2F1, and leads to growth and cell cycle arrest. iDEP helps unveil the multifaceted functions of p53 and the possible involvement of several microRNAs such as miR-92a, miR-504, and miR-30a. In both examples, we validated known molecular pathways and generated novel, testable hypotheses.
conclusionsCombining comprehensive analytic functionalities with massive annotation databases, iDEP ( http://ge-lab.org/idep/ ) enables biologists to easily translate transcriptomic and proteomic data into actionable insights.
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.