ArticleBMC genomics2017
Regulatory network changes between cell lines and their tissues of origin.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 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
43 citing papers in PubMed, 84 citations in OpenAlex.
- Isolation Strategy Matters: How Tissue Processing Shapes the Composition of Placental Extracellular Vesicles.Journal of extracellular biology · 2025Article
- Klotho protein alleviates heart ischemia/reperfusion injury and oxidative stress through regulation of the NOS/MMP pathway.Scientific reports · 2025Article
- Genetic Signatures of Competitive Performance in Burmese Gamecocks: A Transcriptomic Analysis.Biology · 2025Article
- Lineage-specific regulatory evolution: insights from massively parallel reporter assays.Current opinion in genetics & development · 2025Review
- A Distinct miRNA Profile in Intimal Hyperplasia of Failed Arteriovenous Fistulas Reveals Key Pathogenic Pathways.Biomolecules · 2025Article
- Prediction of protein subcellular localization in single cells.Nature methods · 2025Article
- Probing the limits of cis-acting gene regulation using a model of allelic imbalance quantitative trait loci.PLoS genetics · 2025Article
- Uncovering synaptic and cellular nanoarchitecture of brain tissue via seamlessbioRxiv : the preprint server for biology · 2025Article
- SMAD5 as a novel gene for familial pulmonary arterial hypertension.Clinical science (London, England : 1979) · 2025Article
- Transcriptome analyses identify 10 deregulated hub genes and essential molecular mechanisms in early-onset colorectal cancer.Frontiers in oncology · 2025Article
- A ligand-centered framework for γδ T cell activation in colorectal cancer revealed by single-cell and transformer-based perturbation.Frontiers in immunology · 2025Article
- AnFrontiers in genetics · 2025Article
- Patient-matched tumours, plasma, and cell lines reveal tumour microenvironment- and cell culture-specific microRNAs.Biology open · 2024Article
- Article
- Tissue-specific atlas of trans-models for gene regulation elucidates complex regulation patterns.BMC genomics · 2024Article
- Atlas of primary cell-type-specific sequence models of gene expression and variant effects.Cell reports methods · 2023Article
- CIRCUST: A novel methodology for temporal order reconstruction of molecular rhythms; validation and application towards a daily rhythm gene expression atlas in humans.PLoS computational biology · 2023Article
- Three-Dimensional Spheroid Culture of Human Mesenchymal Stem Cells: Offering Therapeutic Advantages and In Vitro Glimpses of the In Vivo State.Stem cells translational medicine · 2023Review
- Efficient transfection of Atlantic salmon primary hepatocyte cells for functional assays and gene editing.G3 (Bethesda, Md.) · 2023Article
- Distinct expression and function of breast cancer metastasis suppressor 1 in mutant P53 glioblastoma.Cellular oncology (Dordrecht, Netherlands) · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 1 country.
Funding
Abstract
backgroundCell lines are an indispensable tool in biomedical research and often used as surrogates for tissues. Although there are recognized important cellular and transcriptomic differences between cell lines and tissues, a systematic overview of the differences between the regulatory processes of a cell line and those of its tissue of origin has not been conducted. The RNA-Seq data generated by the GTEx project is the first available data resource in which it is possible to perform a large-scale transcriptional and regulatory network analysis comparing cell lines with their tissues of origin.
resultsWe compared 127 paired Epstein-Barr virus transformed lymphoblastoid cell lines (LCLs) and whole blood samples, and 244 paired primary fibroblast cell lines and skin samples. While gene expression analysis confirms that these cell lines carry the expression signatures of their primary tissues, albeit at reduced levels, network analysis indicates that expression changes are the cumulative result of many previously unreported alterations in transcription factor (TF) regulation. More specifically, cell cycle genes are over-expressed in cell lines compared to primary tissues, and this alteration in expression is a result of less repressive TF targeting. We confirmed these regulatory changes for four TFs, including SMAD5, using independent ChIP-seq data from ENCODE.
conclusionsOur results provide novel insights into the regulatory mechanisms controlling the expression differences between cell lines and tissues. The strong changes in TF regulation that we observe suggest that network changes, in addition to transcriptional levels, should be considered when using cell lines as models for tissues.
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.