Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA87621 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Toward a functional annotation of the human genome using artificial transcription factors. Keywords: other
2003-12-12 | GSE677 | GEO
Project description:Toward a functional annotation of the human genome using artificial transcription factors.
2010-06-05 | E-GEOD-677 | biostudies-arrayexpress
Project description:Functional genomics of artificial transcription factor-induced iPS cells
| PRJNA350707 | ENA
Project description:Functional annotation of transcriptional factors transactivation domains
| PRJNA471260 | ENA
Project description:Genome-wide functional perturbation of human microsatellite repeats using engineered zinc finger transcription factors
| PRJNA688075 | ENA
Project description:H1975/OSI cell line was induced in vitro through intermittent induction. Cell activity was measured using cell counting kit-8 assay. Uni-omics and multi-omics analyses were conducted on the transcriptomic and proteomic (4D label-free) expression profiles, which involved differential expression analysis, GO functional annotation and KEGG pathway enrichment analysis, correlation analysis of transcription factors, PPI network and Cytoscape analysis.
2023-07-18 | PXD043855 |
Project description:Chavez2009 - a core regulatory network of OCT4 in human embryonic stem cells
A core OCT4-regulated network has been identified as a test case, to analyase stem cell characteristics and cellular differentiation.
This model is described in the article:
In silico identification of a core regulatory network of OCT4 in human embryonic stem cells using an integrated approach.
Chavez L, Bais AS, Vingron M, Lehrach H, Adjaye J, Herwig R
BMC Genomics, 2009, 10:314
Abstract:
BACKGROUND: The transcription factor OCT4 is highly expressed in pluripotent embryonic stem cells which are derived from the inner cell mass of mammalian blastocysts. Pluripotency and self renewal are controlled by a transcription regulatory network governed by the transcription factors OCT4, SOX2 and NANOG. Recent studies on reprogramming somatic cells to induced pluripotent stem cells highlight OCT4 as a key regulator of pluripotency.
RESULTS: We have carried out an integrated analysis of high-throughput data (ChIP-on-chip and RNAi experiments along with promoter sequence analysis of putative target genes) and identified a core OCT4 regulatory network in human embryonic stem cells consisting of 33 target genes. Enrichment analysis with these target genes revealed that this integrative analysis increases the functional information content by factors of 1.3 - 4.7 compared to the individual studies. In order to identify potential regulatory co-factors of OCT4, we performed a de novo motif analysis. In addition to known validated OCT4 motifs we obtained binding sites similar to motifs recognized by further regulators of pluripotency and development; e.g. the heterodimer of the transcription factors C-MYC and MAX, a prerequisite for C-MYC transcriptional activity that leads to cell growth and proliferation.
CONCLUSION: Our analysis shows how heterogeneous functional information can be integrated in order to reconstruct gene regulatory networks. As a test case we identified a core OCT4-regulated network that is important for the analysis of stem cell characteristics and cellular differentiation. Functional information is largely enriched using different experimental results. The de novo motif discovery identified well-known regulators closely connected to the OCT4 network as well as potential new regulators of pluripotency and differentiation. These results provide the basis for further targeted functional studies.
This model is hosted on BioModels Database
and identified
by: MODEL1305010000
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2005-01-01 | MODEL1305010000 | BioModels
Project description:Human iPS cells were differentiated to cholangiocyte-like cells thorugh five phases of endodermal differentiation. Human iPSC were generated by forced expression of the Yamanaka pluripotency factors. We then pursued a stepwise differentiation strategy toward iDCs, using precise temporal exposure to key biliary morphogens, and we characterized the cells, using a variety of morphologic, molecular, cell biologic, functional, and in vivo approaches.
2016-08-25 | E-GEOD-86007 | biostudies-arrayexpress
Project description:Expression data from a new FACS approach isolated hESC derived endoderm cells using transcription factors
| PRJNA130133 | ENA