ArticleNucleic acids research2011
Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 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.
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Who cites it
65 citing papers in PubMed, 112 citations in OpenAlex.
- The role of endolysosomal progranulin and TMEM106B in neurodegenerative diseases.Molecular neurodegeneration · 2025Review
- Progranulin deficiency in the brain: the interplay between neuronal and non-neuronal cells.Translational neurodegeneration · 2025Review
- SCEMENT: scalable and memory efficient integration of large-scale single-cell RNA-sequencing data.Bioinformatics (Oxford, England) · 2025Article
- The role of progranulin in macrophages of a glioblastoma model.Journal of neuro-oncology · 2024Article
- Benzoxazole-derivatives enhance progranulin expression and reverse the aberrant lysosomal proteome caused by GRN haploinsufficiency.Nature communications · 2024Article
- Targeting Progranulin as an Immuno-Neurology Therapeutic Approach.International journal of molecular sciences · 2023Review
- AAV-iScience · 2023Article
- Polymer folding through active processes recreates features of genome organization.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Review
- Differential regulation of progranulin derived granulin peptides.Molecular neurodegeneration · 2022Article
- Regulation of lysosomal trafficking of progranulin by sortilin and prosaposin.Brain communications · 2022Article
- Defects of Nutrient Signaling and Autophagy in Neurodegeneration.Frontiers in cell and developmental biology · 2022Review
- Complex small-world regulatory networks emerge from the 3D organisation of the human genome.Nature communications · 2021Article
- Hierarchical dinucleotide distribution in genome along evolution and its effect on chromatin packing.Life science alliance · 2021Article
- Lysosome dysfunction as a cause of neurodegenerative diseases: Lessons from frontotemporal dementia and amyotrophic lateral sclerosis.Neurobiology of disease · 2021Review
- Tweaking Progranulin Expression: Therapeutic Avenues and Opportunities.Frontiers in molecular neuroscience · 2021Review
- Lysosomal Dysfunction and Other Pathomechanisms in FTLD: Evidence from Progranulin Genetics and Biology.Advances in experimental medicine and biology · 2021Article
- Loss of TMEM106B potentiates lysosomal and FTLD-like pathology in progranulin-deficient mice.EMBO reports · 2020Article
- Loss of TMEM106B and PGRN leads to severe lysosomal abnormalities and neurodegeneration in mice.EMBO reports · 2020Article
- Article
5 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
11 authors at 3 institutions in 1 country.
Funding
Abstract
We collected a massive and heterogeneous dataset of 20 255 gene expression profiles (GEPs) from a variety of human samples and experimental conditions, as well as 8895 GEPs from mouse samples. We developed a mutual information (MI) reverse-engineering approach to quantify the extent to which the mRNA levels of two genes are related to each other across the dataset. The resulting networks consist of 4 817 629 connections among 20 255 transcripts in human and 14 461 095 connections among 45 101 transcripts in mouse, with a inter-species conservation of 12%. The inferred connections were compared against known interactions to assess their biological significance. We experimentally validated a subset of not previously described protein-protein interactions. We discovered co-expressed modules within the networks, consisting of genes strongly connected to each other, which carry out specific biological functions, and tend to be in physical proximity at the chromatin level in the nucleus. We show that the network can be used to predict the biological function and subcellular localization of a protein, and to elucidate the function of a disease gene. We experimentally verified that granulin precursor (GRN) gene, whose mutations cause frontotemporal lobar degeneration, is involved in lysosome function. We have developed an online tool to explore the human and mouse gene networks.
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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.