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Origins of Transcriptional Transition: Balance between Upstream and Downstream Regulatory Gene Sequences

Sala, Adrien ; Shoaib, Muhammad ; Anufrieva, Olga ; [et al.]

American Society for Microbiology ; 2015

In: mBio Vol. 6, No. 1 ( 2015-02-27)

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In: mBio, American Society for Microbiology, Vol. 6, No. 1 ( 2015-02-27)

Abstract: By measuring individual mRNA production at the single-cell level, we investigated the lac promoter transcriptional transition during cell growth phases. In exponential phase, variation in transition rate generates two mixed phenotypes producing low and high numbers of mRNAs by modulating the burst frequency and size. Independent activation of the regulatory gene sequence does not produce bimodal populations at the mRNA level, while it does when activated together through the coordination of upstream/downstream promoter sequences (URS/DRS). Time-lapse microscopy of mRNAs for lac and a lac variant promoter confirm this observation. Activation of the URS/DRS elements of the promoter reveals a counterplay behavior during cell phases. The promoter transition rate coupled with cell phases determines the mRNA and transcriptional noise. We further show that bias in partitioning of RNA does not lead to phenotypic switching. Our results demonstrate that the balance between URS and DRS in transcription regulation is determining the population diversity.

Type of Medium: Online Resource

ISSN: 2161-2129 , 2150-7511

URL: Article

DOI: 10.1128/mBio.02182-14

Language: English

Publisher: American Society for Microbiology

Publication Date: 2015

detail.hit.zdb_id: 2557172-2

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Driver Fusions and Their Implications in the Development and Treatment of Human Cancers

Gao, Qingsong ; Liang, Wen-Wei ; Foltz, Steven M. ; [et al.]

Elsevier BV ; 2018

In: Cell Reports Vol. 23, No. 1 ( 2018-04), p. 227-238.e3

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In: Cell Reports, Elsevier BV, Vol. 23, No. 1 ( 2018-04), p. 227-238.e3

Type of Medium: Online Resource

ISSN: 2211-1247

URL: Article

DOI: 10.1016/j.celrep.2018.03.050

Language: English

Publisher: Elsevier BV

Publication Date: 2018

detail.hit.zdb_id: 2649101-1

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Typical and atypical domain combinations in human protein kinases: functions, disease causing mutations and conservation in other primates

Rakshambikai, Ramaswamy ; Manoharan, Malini ; Gnanavel, Mutharasu ; [et al.]

Royal Society of Chemistry (RSC) ; 2015

In: RSC Advances Vol. 5, No. 32 ( 2015), p. 25132-25148

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In: RSC Advances, Royal Society of Chemistry (RSC), Vol. 5, No. 32 ( 2015), p. 25132-25148

Type of Medium: Online Resource

ISSN: 2046-2069

URL: Article

DOI: 10.1039/C4RA11685B

Language: English

Publisher: Royal Society of Chemistry (RSC)

Publication Date: 2015

detail.hit.zdb_id: 2623224-8

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Identification of novel sweet protein for nutritional applications

Mutharasu, Gnanavel ; Peddha, Muthukumar Serva

Biomedical Informatics ; 2011

In: Bioinformation Vol. 7, No. 3 ( 2011-09-28), p. 112-114

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In: Bioinformation, Biomedical Informatics, Vol. 7, No. 3 ( 2011-09-28), p. 112-114

Type of Medium: Online Resource

ISSN: 0973-8894 , 0973-2063

URL: Issue

URL: Journal

URL: Article

DOI: 10.6026/007.003

DOI: 10.6026/bioinformation

DOI: 10.6026/97320630007112

Language: Unknown

Publisher: Biomedical Informatics

Publication Date: 2011

detail.hit.zdb_id: 2203786-X

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168 Classification of protein sequences with special references to multi-domain systems

Mehrotra, Prachi ; Bhaskara, Ramachandra M. ; Gnanavel, Mutharasu ; [et al.]

Informa UK Limited ; 2015

In: Journal of Biomolecular Structure and Dynamics Vol. 33, No. sup1 ( 2015-05-18), p. 110-110

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In: Journal of Biomolecular Structure and Dynamics, Informa UK Limited, Vol. 33, No. sup1 ( 2015-05-18), p. 110-110

Type of Medium: Online Resource

ISSN: 0739-1102 , 1538-0254

URL: Article

DOI: 10.1080/07391102.2015.1032805

Language: English

Publisher: Informa UK Limited

Publication Date: 2015

detail.hit.zdb_id: 2085732-9

SSG: 12

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Identifying the miRNA Signature Association with Aging-Related Senescence in Glioblastoma

Gnanavel, Mutharasu ; Murugesan, Akshaya ; Konda Mani, Saravanan ; [et al.]

MDPI AG ; 2021

In: International Journal of Molecular Sciences Vol. 22, No. 2 ( 2021-01-06), p. 517-

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In: International Journal of Molecular Sciences, MDPI AG, Vol. 22, No. 2 ( 2021-01-06), p. 517-

Abstract: Glioblastoma (GBM) is the most common malignant brain tumor and its malignant phenotypic characteristics are classified as grade IV tumors. Molecular interactions, such as protein–protein, protein–ncRNA, and protein–peptide interactions are crucial to transfer the signaling communications in cellular signaling pathways. Evidences suggest that signaling pathways of stem cells are also activated, which helps the propagation of GBM. Hence, it is important to identify a common signaling pathway that could be visible from multiple GBM gene expression data. microRNA signaling is considered important in GBM signaling, which needs further validation. We performed a high-throughput analysis using micro array expression profiles from 574 samples to explore the role of non-coding RNAs in the disease progression and unique signaling communication in GBM. A series of computational methods involving miRNA expression, gene ontology (GO) based gene enrichment, pathway mapping, and annotation from metabolic pathways databases, and network analysis were used for the analysis. Our study revealed the physiological roles of many known and novel miRNAs in cancer signaling, especially concerning signaling in cancer progression and proliferation. Overall, the results revealed a strong connection with stress induced senescence, significant miRNA targets for cell cycle arrest, and many common signaling pathways to GBM in the network.

Type of Medium: Online Resource

ISSN: 1422-0067

URL: Article

DOI: 10.3390/ijms22020517

Language: English

Publisher: MDPI AG

Publication Date: 2021

detail.hit.zdb_id: 2019364-6

SSG: 12

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The relationship between classification of multi-domain proteins using an alignment-free approach and their functions: a case study with immunoglobulins

Bhaskara, Ramachandra M. ; Mehrotra, Prachi ; Rakshambikai, Ramaswamy ; [et al.]

Royal Society of Chemistry (RSC) ; 2014

In: Molecular BioSystems Vol. 10, No. 5 ( 2014), p. 1082-

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In: Molecular BioSystems, Royal Society of Chemistry (RSC), Vol. 10, No. 5 ( 2014), p. 1082-

Type of Medium: Online Resource

ISSN: 1742-206X , 1742-2051

URL: Article

DOI: 10.1039/c3mb70443b

Language: English

Publisher: Royal Society of Chemistry (RSC)

Publication Date: 2014

detail.hit.zdb_id: 2188635-0

SSG: 12

SSG: 15,3

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Hybrid and Rogue Kinases Encoded in the Genomes of Model Eukaryotes

Rakshambikai, Ramaswamy ; Gnanavel, Mutharasu ; Srinivasan, Narayanaswamy ; [et al.]

Public Library of Science (PLoS) ; 2014

In: PLoS ONE Vol. 9, No. 9 ( 2014-9-25), p. e107956-

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In: PLoS ONE, Public Library of Science (PLoS), Vol. 9, No. 9 ( 2014-9-25), p. e107956-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0107956

DOI: 10.1371/journal.pone.0107956.g001

DOI: 10.1371/journal.pone.0107956.g002

DOI: 10.1371/journal.pone.0107956.g003

DOI: 10.1371/journal.pone.0107956.g004

DOI: 10.1371/journal.pone.0107956.g005

DOI: 10.1371/journal.pone.0107956.g006

DOI: 10.1371/journal.pone.0107956.g007

DOI: 10.1371/journal.pone.0107956.s001

DOI: 10.1371/journal.pone.0107956.s002

DOI: 10.1371/journal.pone.0107956.s003

DOI: 10.1371/journal.pone.0107956.s004

DOI: 10.1371/journal.pone.0107956.s005

DOI: 10.1371/journal.pone.0107956.s006

DOI: 10.1371/journal.pone.0107956.s007

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2014

detail.hit.zdb_id: 2267670-3

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Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors

Sala, Adrien ; Shoaib, Muhammad ; Anufrieva, Olga ; [et al.]

IOP Publishing ; 2015

In: Physical Biology Vol. 12, No. 3 ( 2015-05-19), p. 036003-

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In: Physical Biology, IOP Publishing, Vol. 12, No. 3 ( 2015-05-19), p. 036003-

Type of Medium: Online Resource

ISSN: 1478-3975

URL: Article

DOI: 10.1088/1478-3975/12/3/036003

Language: Unknown

Publisher: IOP Publishing

Publication Date: 2015

detail.hit.zdb_id: 2133216-2

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CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Gnanavel, Mutharasu ; Mehrotra, Prachi ; Rakshambikai, Ramaswamy ; [et al.]

Springer Science and Business Media LLC ; 2014

In: BMC Bioinformatics Vol. 15, No. 1 ( 2014-12)

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In: BMC Bioinformatics, Springer Science and Business Media LLC, Vol. 15, No. 1 ( 2014-12)

Type of Medium: Online Resource

ISSN: 1471-2105

URL: Article

DOI: 10.1186/1471-2105-15-343

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2014

detail.hit.zdb_id: 2041484-5

SSG: 12

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