ArticlePLoS computational biology2010
Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 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
16 citing papers in PubMed, 30 citations in OpenAlex.
- Establishing a model composed of immune-related gene-modules to predict tumor immunotherapy response.Scientific reports · 2024Article
- Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species.Bioinformatics (Oxford, England) · 2021Article
- A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome.PLoS computational biology · 2018Article
- Chemical compound-based direct reprogramming for future clinical applications.Bioscience reports · 2018Review
- Krüppel-like factors in mammalian stem cells and development.Development (Cambridge, England) · 2017Review
- Article
- Clinical significance of the stem cell gene Oct-4 in cervical cancer.Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine · 2014Article
- Article
- Divergence of mammalian higher order chromatin structure is associated with developmental loci.PLoS computational biology · 2013Article
- Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria.BMC genomics · 2013Article
- CORRELATION PURSUIT: FORWARD STEPWISE VARIABLE SELECTION FOR INDEX MODELS.Journal of the Royal Statistical Society. Series B, Statistical methodology · 2012Article
- A gene expression profile of stem cell pluripotentiality and differentiation is conserved across diverse solid and hematopoietic cancers.Genome biology · 2012Article
- Towards an evolutionary model of transcription networks.PLoS computational biology · 2011Article
- COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms.Nucleic acids research · 2011Article
- ExprEssence--revealing the essence of differential experimental data in the context of an interaction/regulation net-work.BMC systems biology · 2010Article
- Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering.Genome biology · 2010Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Complex interactions between genes or proteins contribute substantially to phenotypic evolution. We present a probabilistic model and a maximum likelihood approach for cross-species clustering analysis and for identification of conserved as well as species-specific co-expression modules. This model enables a "soft" cross-species clustering (SCSC) approach by encouraging but not enforcing orthologous genes to be grouped into the same cluster. SCSC is therefore robust to obscure orthologous relationships and can reflect different functional roles of orthologous genes in different species. We generated a time-course gene expression dataset for differentiating mouse embryonic stem (ES) cells, and compiled a dataset of published gene expression data on differentiating human ES cells. Applying SCSC to analyze these datasets, we identified conserved and species-specific gene regulatory modules. Together with protein-DNA binding data, an SCSC cluster specifically induced in murine ES cells indicated that the KLF2/4/5 transcription factors, although critical to maintaining the pluripotent phenotype in mouse ES cells, were decoupled from the OCT4/SOX2/NANOG regulatory module in human ES cells. Two of the target genes of murine KLF2/4/5, LIN28 and NODAL, were rewired to be targets of OCT4/SOX2/NANOG in human ES cells. Moreover, by mapping SCSC clusters onto KEGG signaling pathways, we identified the signal transduction components that were induced in pluripotent ES cells in either a conserved or a species-specific manner. These results suggest that the pluripotent cell identity can be established and maintained through more than one gene regulatory network.
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.