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  1. Article ; Online: PSCRIdb: A database of regulatory interactions and networks of pluripotent stem cell lines.

    Banerjee, Krishnendu / Jana, Tanmoy / Ghosh, Zhumur / Saha, Sudipto

    Journal of biosciences

    2020  Volume 45

    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 ... ...

    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.
    MeSH term(s) Animals ; Cell Line ; Computational Biology ; Databases, Factual ; Embryonic Stem Cells/metabolism ; Epigenesis, Genetic ; Gene Expression Regulation, Developmental ; Gene Regulatory Networks ; Humans ; Induced Pluripotent Stem Cells/metabolism ; Mice ; MicroRNAs/genetics ; MicroRNAs/metabolism ; Pluripotent Stem Cells/metabolism ; Protein Interaction Mapping ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Transcription Factors/genetics
    Chemical Substances MicroRNAs ; RNA, Messenger ; Transcription Factors
    Language English
    Publishing date 2020-04-28
    Publishing country India
    Document type Journal Article
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1907: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)

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

    Banerjee, Krishnendu / Jana, Tanmoy / Ghosh, Zhumur / Saha, Sudipto

    Journal of biosciences. 2020 Dec., v. 45, no. 1

    2020  

    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 ... ...

    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.
    Keywords carcinoma ; databases ; epigenetics ; humans ; mice ; multiomics
    Language English
    Dates of publication 2020-12
    Size p. 53.
    Publishing place Springer India
    Document type Article
    ZDB-ID 756157-x
    ISSN 0973-7138 ; 0250-5991
    ISSN (online) 0973-7138
    ISSN 0250-5991
    DOI 10.1007/s12038-020-00027-4
    Database NAL-Catalogue (AGRICOLA)

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    In stock of ZB MED Bonn / Germany

    Z 5290: Show issues

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  3. Article ; Online: In silico modeling of phosphorylation dependent and independent c-Myc degradation.

    Chakravorty, Debangana / Banerjee, Krishnendu / Mapder, Tarunendu / Saha, Sudipto

    BMC bioinformatics

    2019  Volume 20, Issue 1, Page(s) 230

    Abstract: Background: c-Myc plays an important role in cell proliferation, cell growth and in differentiation, making it a key regulator for carcinogenesis and pluripotency. Tight control of c-myc turnover is required by ubiquitin-mediated degradation. This is ... ...

    Abstract Background: c-Myc plays an important role in cell proliferation, cell growth and in differentiation, making it a key regulator for carcinogenesis and pluripotency. Tight control of c-myc turnover is required by ubiquitin-mediated degradation. This is achieved in the system by two F-box proteins Skp2 and FBXW7.
    Results: Dynamic modelling technique was used to build two exclusive models for phosphorylation dependent degradation of Myc by FBXW7 (Model 1) and phosphorylation independent degradation by Skp2 (Model 2). Sensitivity analysis performed on these two models revealed that these models were corroborating experimental studies. It was also seen that Model 1 was more robust and perhaps more efficient in degrading c-Myc. These results questioned the existence of the two models in the system and to answer the question a combined model was hypothesised which had a decision making switch. The combined model had both Skp2 and FBXW7 mediated degradation where again the latter played a more important role. This model was able to achieve the lowest levels of ubiquitylated Myc and therefore functioned most efficiently in degradation of Myc.
    Conclusion: In this report, c-Myc degradation by two F-box proteins was mathematically evaluated based on the importance of c-Myc turnover. The study was performed in a homeostatic system and therefore, prompts the exploration of c-Myc degradation in cancer state and in pluripotent state.
    MeSH term(s) Cell Proliferation ; Computer Simulation/standards ; Humans ; Phosphorylation/physiology ; Proto-Oncogene Proteins c-myc/metabolism
    Chemical Substances Proto-Oncogene Proteins c-myc
    Language English
    Publishing date 2019-05-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/s12859-019-2846-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: GFI1/HDAC1-axis differentially regulates immunosuppressive CD73 in human tumor-associated FOXP3

    Roy, Dia / Bose, Sayantan / Pati, Subhadip / Guin, Aharna / Banerjee, Krishnendu / Saha, Sudipto / Singhal, Ayush K / Chakraborty, Jayati / Sarkar, Diptendra K / Sa, Gaurisankar

    European journal of immunology

    2021  Volume 51, Issue 5, Page(s) 1206–1217

    Abstract: Plasticity between Th17 and Treg cells is regarded as a crucial determinant of tumor-associated immunosuppression. Classically Th17 cells mediate inflammatory responses through production of cytokine IL17. Recently, Th17 cells have also been shown to ... ...

    Abstract Plasticity between Th17 and Treg cells is regarded as a crucial determinant of tumor-associated immunosuppression. Classically Th17 cells mediate inflammatory responses through production of cytokine IL17. Recently, Th17 cells have also been shown to acquire suppressive phenotypes in tumor microenvironment. However, the mechanism by which they acquire such immunosuppressive properties is still elusive. Here, we report that in tumor microenvironment Th17 cell acquires immunosuppressive properties by expressing Treg lineage-specific transcription factor FOXP3 and ectonucleotidase CD73. We designate this cell as Th17reg cell and perceive that such immunosuppressive property is dependent on CD73. It was observed that in classical Th17 cell, GFI1 recruits HDAC1 to change the euchromatin into tightly-packed heterochromatin at the proximal-promoter region of CD73 to repress its expression. Whereas in Th17reg cells GFI1 cannot get access to CD73-promoter due to heterochromatin state at its binding site and, thus, cannot recruit HDAC1, failing to suppress the expression of CD73.
    MeSH term(s) 5'-Nucleotidase/metabolism ; Cytokines/metabolism ; DNA-Binding Proteins/metabolism ; Forkhead Transcription Factors/metabolism ; Gene Expression Regulation, Neoplastic ; Histone Deacetylase 1/metabolism ; Humans ; Immunomodulation ; Lymphocytes, Tumor-Infiltrating/immunology ; Lymphocytes, Tumor-Infiltrating/metabolism ; Promoter Regions, Genetic ; Signal Transduction ; T-Lymphocytes, Regulatory/immunology ; T-Lymphocytes, Regulatory/metabolism ; Th17 Cells/immunology ; Th17 Cells/metabolism ; Transcription Factors/metabolism ; Tumor Microenvironment/genetics ; Tumor Microenvironment/immunology
    Chemical Substances Cytokines ; DNA-Binding Proteins ; FOXP3 protein, human ; Forkhead Transcription Factors ; GFI1 protein, human ; Transcription Factors ; 5'-Nucleotidase (EC 3.1.3.5) ; HDAC1 protein, human (EC 3.5.1.98) ; Histone Deacetylase 1 (EC 3.5.1.98)
    Language English
    Publishing date 2021-02-17
    Publishing country Germany
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 120108-6
    ISSN 1521-4141 ; 0014-2980
    ISSN (online) 1521-4141
    ISSN 0014-2980
    DOI 10.1002/eji.202048892
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 489: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (1.OG)
    ab Jg. 2022: Lesesaal (EG)
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