Abstract
Pluripotency in stem cells is regulated by a complex network between the transcription factors, signaling molecules, mRNAs, and epigenetic regulators like non-coding RNAs. Different pluripotent stem cell (PSC) lines were isolated and characterized to study the regulatory network topology to understand the mechanism that control developmental potential of pluripotent cells. PSCRIdb is a manually curated database of regulatory interactions including protein–protein, protein–DNA, gene–gene, and miRNA–mRNA interactions in mouse and human pluripotent stem cells including embryonic stem cells and embryonic carcinoma cells. At present, 22 different mouse and human pluripotent stem-cell-line-specific regulatory interactions are compiled in the database. Detailed information of the four types of interaction data are presented in tabular format and graphical network view in Cytoscape layout. The database is available at http://bicresources.jcbose.ac.in/ssaha4/pscridb. The database contains 3037 entries of experimentally validated molecular interactions that can be useful for systematic study of pluripotency integrating multi-omics data. In summary, the database can be a useful resource for identification of regulatory networks present in different pluripotent stem cell lines.
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Abbreviations
- PSC:
-
Pluripotent stem cell
- ChIP-chip/seq:
-
Chromatin immunoprecipitation followed by microarrays/sequencing
- AP-MS:
-
Affinity-purification followed by mass-spectrometry
- IP-MS:
-
Immunoprecipitation followed by mass-spectrometry
- ChIP-PET:
-
Chromatinb immunoprecipitation followed by paired-end tag sequencing
- LOI:
-
Loss of imprinting
- PIRN:
-
Pluripotent integrated regulatory network
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Acknowledgements
The authors acknowledge Division of Bioinformatics, Bose Institute, Kolkata, for providing the infrastructure. This work was supported by Indian Council of Medical Research (ICMR), India (ICMR-BIC/12(30)/2012).
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Communicated by BJ RAO.
Corresponding editor: BJ Rao
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Banerjee, K., Jana, T., Ghosh, Z. et al. PSCRIdb: A database of regulatory interactions and networks of pluripotent stem cell lines. J Biosci 45, 53 (2020). https://doi.org/10.1007/s12038-020-00027-4
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DOI: https://doi.org/10.1007/s12038-020-00027-4