ArticleBMC bioinformatics2006
Beyond microarrays: find key transcription factors controlling signal transduction pathways.
Article in BMC bioinformatics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 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
49 citing papers in PubMed, 98 citations in OpenAlex.
- Comprehensive transcriptome, miRNA and kinome profiling identifies new treatment options for personalized lung cancer therapy.Clinical and translational medicine · 2025Article
- Epigenome-Wide Changes in the Cell Layers of the Vein Wall When Exposing the Venous Endothelium to Oscillatory Shear Stress.Epigenomes · 2023Article
- Transcriptome Analysis Reveals Intrinsic Proinflammatory Signaling in Healthy African American Skin.The Journal of investigative dermatology · 2022Article
- The Jun-dependent axon regeneration gene program: Jun promotes regeneration over plasticity.Human molecular genetics · 2022Article
- WNT11/ROR2 signaling is associated with tumor invasion and poor survival in breast cancer.Journal of experimental & clinical cancer research : CR · 2021Article
- Expression dynamics of HAND1/2 in in vitro human cardiomyocyte differentiation.Stem cell reports · 2021Article
- IGFBP2 Is a Potential Master Regulator Driving the Dysregulated Gene Network Responsible for Short Survival in Glioblastoma Multiforme.Frontiers in genetics · 2021Article
- Using systems medicine to identify a therapeutic agent with potential for repurposing in inflammatory bowel disease.Disease models & mechanisms · 2020Article
- Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer.BMC bioinformatics · 2019Article
- Mycoplasma hyorhinis reduces sensitivity of human lung carcinoma cells to Nutlin-3 and promotes their malignant phenotype.Journal of cancer research and clinical oncology · 2018Article
- Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3.BMC medical genomics · 2018Article
- Glial responses during epileptogenesis in Mus musculus point to potential therapeutic targets.PloS one · 2018Article
- Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis.Current pharmaceutical design · 2018Article
- Relevance of iPSC-derived human PGC-like cells at the surface of embryoid bodies to prechemotaxis migrating PGCs.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- CD169Science immunology · 2017Article
- The genomic architecture of mastitis resistance in dairy sheep.BMC genomics · 2017Article
- Data on master regulators and transcription factor binding sites found by upstream analysis of multi-omics data on methotrexate resistance of colon cancer.Data in brief · 2017Article
- Deep Sequencing Transcriptome Analysis of Murine Wound Healing: Effects of a Multicomponent, Multitarget Natural Product Therapy-Tr14.Frontiers in molecular biosciences · 2017Article
- Pathways of aging: comparative analysis of gene signatures in replicative senescence and stress induced premature senescence.BMC genomics · 2016Article
- Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer.EuPA open proteomics · 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
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMassive gene expression changes in different cellular states measured by microarrays, in fact, reflect just an "echo" of real molecular processes in the cells. Transcription factors constitute a class of the regulatory molecules that typically require posttranscriptional modifications or ligand binding in order to exert their function. Therefore, such important functional changes of transcription factors are not directly visible in the microarray experiments.
resultsWe developed a novel approach to find key transcription factors that may explain concerted expression changes of specific components of the signal transduction network. The approach aims at revealing evidence of positive feedback loops in the signal transduction circuits through activation of pathway-specific transcription factors. We demonstrate that promoters of genes encoding components of many known signal transduction pathways are enriched by binding sites of those transcription factors that are endpoints of the considered pathways. Application of the approach to the microarray gene expression data on TNF-alpha stimulated primary human endothelial cells helped to reveal novel key transcription factors potentially involved in the regulation of the signal transduction pathways of the cells.
conclusionWe developed a novel computational approach for revealing key transcription factors by knowledge-based analysis of gene expression data with the help of databases on gene regulatory networks (TRANSFAC and TRANSPATH. The corresponding software and databases are available at http://www.gene-regulation.com.
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.