scholarly journals Genomic analysis of xCT-regulatory network in KSHV + primary effusion lymphomas

Genomics Data ◽  
2016 ◽  
Vol 8 ◽  
pp. 16-17
Author(s):  
Zhiqiang Qin ◽  
Yueyu Cao ◽  
Lu Dai
Keyword(s):  
Regulatory Network ◽  
Genomic Analysis ◽  
Primary Effusion Lymphomas

Genomic analysis of regulatory network dynamics reveals large topological changes

Nature ◽  
2004 ◽  
Vol 431 (7006) ◽  
pp. 308-312 ◽  
Author(s):  
Nicholas M. Luscombe ◽  
M. Madan Babu ◽  
Haiyuan Yu ◽  
Michael Snyder ◽  
Sarah A. Teichmann ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Network Dynamics ◽  
Genomic Analysis ◽  
Topological Changes

scholarly journals Functional Genomic Analysis of the let-7 Regulatory Network in Caenorhabditis elegans

PLoS Genetics ◽  
2013 ◽  
Vol 9 (3) ◽  
pp. e1003353 ◽  
Author(s):  
Shaun E. Hunter ◽  
Emily F. Finnegan ◽  
Dimitrios G. Zisoulis ◽  
Michael T. Lovci ◽  
Katya V. Melnik-Martinez ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Regulatory Network ◽  
Genomic Analysis ◽  
Functional Genomic ◽  
Functional Genomic Analysis

scholarly journals Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture

2009 ◽  
Vol 5 (1) ◽  
pp. 294 ◽  
Author(s):  
Raja Jothi ◽  
S Balaji ◽  
Arthur Wuster ◽  
Joshua A Grochow ◽  
Jörg Gsponer ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Regulatory Network ◽  
Network Architecture ◽  
Genomic Analysis

scholarly journals iRegNet3D: three-dimensional integrated regulatory network for the genomic analysis of coding and non-coding disease mutations

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Siqi Liang ◽  
Nathaniel D. Tippens ◽  
Yaoda Zhou ◽  
Matthew Mort ◽  
Peter D. Stenson ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Three Dimensional ◽  
Genomic Analysis ◽  
Disease Mutations

scholarly journals Cancer-specific mutation of GATA3 disrupts the transcriptional regulatory network governed by Estrogen Receptor alpha, FOXA1 and GATA3

2020 ◽  
Vol 48 (9) ◽  
pp. 4756-4768 ◽  
Author(s):  
Motoki Takaku ◽  
Sara A Grimm ◽  
Bony De Kumar ◽  
Brian D Bennett ◽  
Paul A Wade
Keyword(s):  
Breast Cancer ◽  
Estrogen Receptor ◽  
Regulatory Network ◽  
Cell Biology ◽  
Estrogen Receptor Alpha ◽  
Transcriptional Regulatory Network ◽  
Genomic Analysis ◽  
Receptor Alpha ◽  
Mutant Cells

Abstract Estrogen receptors (ER) are activated by the steroid hormone 17β-estradiol. Estrogen receptor alpha (ER-α) forms a regulatory network in mammary epithelial cells and in breast cancer with the transcription factors FOXA1 and GATA3. GATA3 is one of the most frequently mutated genes in breast cancer and is capable of specifying chromatin localization of FOXA1 and ER-α. How GATA3 mutations found in breast cancer impact genomic localization of ER-α and the transcriptional network downstream of ER-α and FOXA1 remains unclear. Here, we investigate the function of a recurrent patient-derived GATA3 mutation (R330fs) on this regulatory network. Genomic analysis indicates that the R330fs mutant can disrupt localization of ER-α and FOXA1. Loci co-bound by all three factors are enriched for genes integral to mammary gland development as well as epithelial cell biology. This gene set is differentially regulated in GATA3 mutant cells in culture and in tumors bearing similar mutations in vivo. The altered distribution of ER-α and FOXA1 in GATA3-mutant cells is associated with altered chromatin architecture, which leads to differential gene expression. These results suggest an active role for GATA3 zinc finger 2 mutants in ER-α positive breast tumors.

scholarly journals GATA3 mutation disrupts a functional network governed by estrogen receptor, FOXA1 and GATA3

2019 ◽  
Author(s):  
Motoki Takaku ◽  
Sara A. Grimm ◽  
Bony De Kumar ◽  
Brian D. Bennett ◽  
Paul A. Wade
Keyword(s):  
Transcription Factors ◽  
Regulatory Network ◽  
Genomic Analysis ◽  
Active Role ◽  
Cooperative Action ◽  
Er Positive ◽  
17Β Estradiol ◽  
Differential Gene ◽  
Gata3 Mutation ◽  
Mutant Cells

AbstractEstrogen receptors (ER) are part of the nuclear receptor superfamily of transcription factors and are activated by the steroid hormone 17β-estradiol. ER forms a regulatory network in conjunction with other transcription factors, such as FOXA1 and GATA3. GATA3 has been identified as one of the most frequently mutated genes in breast cancer and is capable of specifying chromatin localization of FOXA1 and ER. How GATA3 mutations impact this transcriptional network is unknown. Here we investigate the function of one of the recurrent patient-derived GATA3 mutations (R330fs) on this regulatory network. Genomic analysis indicates that the R330fs mutant can disrupt the cooperative action of ER, FOXA1, and GATA3, and induce a change in chromatin localization of these factors. Relocalization of ER and FOXA1 is associated with altered chromatin architecture, which leads to differential gene expression in GATA3 mutant cells. These results suggest an active role for GATA3 mutants in ER positive breast tumors.

scholarly journals Genomic analysis of xCT-mediated regulatory network: identification of novel targets against AIDS-associated lymphoma

Oncotarget ◽  
2015 ◽  
Vol 6 (14) ◽  
pp. 12710-12722 ◽  
Author(s):  
Lu Dai ◽  
Yueyu Cao ◽  
Yihan Chen ◽  
Johnan A.R. Kaleeba ◽  
Jovanny Zabaleta ◽  
...  
Keyword(s):  
Regulatory Network ◽  
Genomic Analysis ◽  
Network Identification ◽  
Novel Targets

Genomic analysis of C-type lectins

2002 ◽  
Vol 69 ◽  
pp. 59-72 ◽  
Author(s):  
Kurt Drickamer ◽  
Andrew J. Fadden
Keyword(s):  
Biological Effects ◽  
Cell Signalling ◽  
Genomic Analysis ◽  
Binding Activity ◽  
Immunoglobulin Superfamily ◽  
Carbohydrate Binding ◽  
Carbohydrate Recognition ◽  
Calcium Dependent ◽  
Binding Domains ◽  
Carbohydrate Recognition Domains

Many biological effects of complex carbohydrates are mediated by lectins that contain discrete carbohydrate-recognition domains. At least seven structurally distinct families of carbohydrate-recognition domains are found in lectins that are involved in intracellular trafficking, cell adhesion, cell–cell signalling, glycoprotein turnover and innate immunity. Genome-wide analysis of potential carbohydrate-binding domains is now possible. Two classes of intracellular lectins involved in glycoprotein trafficking are present in yeast, model invertebrates and vertebrates, and two other classes are present in vertebrates only. At the cell surface, calcium-dependent (C-type) lectins and galectins are found in model invertebrates and vertebrates, but not in yeast; immunoglobulin superfamily (I-type) lectins are only found in vertebrates. The evolutionary appearance of different classes of sugar-binding protein modules parallels a development towards more complex oligosaccharides that provide increased opportunities for specific recognition phenomena. An overall picture of the lectins present in humans can now be proposed. Based on our knowledge of the structures of several of the C-type carbohydrate-recognition domains, it is possible to suggest ligand-binding activity that may be associated with novel C-type lectin-like domains identified in a systematic screen of the human genome. Further analysis of the sequences of proteins containing these domains can be used as a basis for proposing potential biological functions.

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