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PSCRIdb: A database of regulatory interactions and networks of pluripotent stem cell lines

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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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Authors and Affiliations

  1. Division of Bioinformatics, Bose Institute, Kolkata, India

    Krishnendu Banerjee, Tanmoy Jana, Zhumur Ghosh & Sudipto Saha

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  1. Krishnendu Banerjee
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  2. Tanmoy Jana
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  3. Zhumur Ghosh
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  4. Sudipto Saha
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Corresponding author

Correspondence to Sudipto Saha.

Additional information

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

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