scholarly journals An integrated transcriptomic and comparative genomic analysis of differential gene expression in Arctic charr (Salvelinus alpinus) following seawater exposure

2014 ◽  
Vol 217 (22) ◽  
pp. 4029-4042 ◽  
Author(s):  
J. D. Norman ◽  
M. M. Ferguson ◽  
R. G. Danzmann
Keyword(s):  
Gene Expression ◽  
Differential Gene Expression ◽  
Salvelinus Alpinus ◽  
Arctic Charr ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Differential Gene

scholarly journals AmpDI Is Involved in Expression of the Chromosomal L1 and L2 β-Lactamases of Stenotrophomonas maltophilia

2009 ◽  
Vol 53 (7) ◽  
pp. 2902-2907 ◽  
Author(s):  
Tsuey-Ching Yang ◽  
Yi-Wei Huang ◽  
Rouh-Mei Hu ◽  
Shao-Cheng Huang ◽  
Yu-Tzu Lin
Keyword(s):  
Gene Expression ◽  
Pseudomonas Aeruginosa ◽  
Stenotrophomonas Maltophilia ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Genomic Context ◽  
One Step ◽  
L1 And L2

ABSTRACT Two ampD homologues, ampD I and ampD II, of Stenotrophomonas maltophilia have been cloned and analyzed. Comparative genomic analysis revealed that the genomic context of the ampD II genes is quite different, whereas that of the ampD I genes is more conserved in S. maltophilia strains. The ampD system of S. maltophilia is distinct from that of the Enterobacteriaceae and Pseudomonas aeruginosa in three respects. (i) AmpDI of S. maltophilia is not encoded in an ampDE operon, in contrast to what happens in the Enterobacteriaceae and P. aeruginosa. (ii) The AmpD systems of the Enterobacteriaceae and P. aeruginosa are generally involved in the regulation of ampR-linked ampC gene expression, while AmpDI of S. maltophilia is responsible for the regulation of two intrinsic β-lactamase genes, of which the L2 gene, but not the L1 gene, is linked to ampR. (iii) S. maltophilia exhibits a one-step L1 and L2 gene derepression model involving ampD I, distinct from the two- or three-step derepression of the Enterobacteriaceae and P. aeruginosa. Moreover, the ampD I and ampD II genes are constitutively expressed and not regulated by the inducer and AmpR protein, and the expression of ampD II is weaker than that of ampD I. Finally, AmpDII is not associated with the derepression of β-lactamases, and its role in S. maltophilia remains unclear.

The fmo genes of Caenorhabditis elegans and C. briggsae: characterisation, gene expression and comparative genomic analysis

Gene ◽  
2005 ◽  
Vol 346 ◽  
pp. 83-96 ◽  
Author(s):  
Mark I.R. Petalcorin ◽  
George W. Joshua ◽  
Paul-Michael Agapow ◽  
Colin T. Dolphin
Keyword(s):  
Gene Expression ◽  
Caenorhabditis Elegans ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic

Computational genomic analysis of PARK7 interactome reveals high BBS1 gene expression as a prognostic factor favoring survival in malignant pleural mesothelioma

2015 ◽  
Vol 309 (7) ◽  
pp. L677-L686 ◽  
Author(s):  
Georgios D. Vavougios ◽  
Evgeniy I. Solenov ◽  
Chrissi Hatzoglou ◽  
Galina S. Baturina ◽  
Liubov E. Katkova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Overall Survival ◽  
Differential Gene Expression ◽  
Malignant Pleural Mesothelioma ◽  
Meta Analysis ◽  
Genomic Analysis ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Pleural Mesothelioma ◽  
Differential Gene

The aim of our study was to assess the differential gene expression of Parkinson protein 7 (PARK7) interactome in malignant pleural mesothelioma (MPM) using data mining techniques to identify novel candidate genes that may play a role in the pathogenicity of MPM. We constructed the PARK7 interactome using the ConsensusPathDB database. We then interrogated the Oncomine Cancer Microarray database using the Gordon Mesothelioma Study, for differential gene expression of the PARK7 interactome. In ConsensusPathDB, 38 protein interactors of PARK7 were identified. In the Gordon Mesothelioma Study, 34 of them were assessed out of which SUMO1, UBC3, KIAA0101, HDAC2, DAXX, RBBP4, BBS1, NONO, RBBP7, HTRA2, and STUB1 were significantly overexpressed whereas TRAF6 and MTA2 were significantly underexpressed in MPM patients ( network 2). Furthermore, Kaplan-Meier analysis revealed that MPM patients with high BBS1 expression had a median overall survival of 16.5 vs. 8.7 mo of those that had low expression. For validation purposes, we performed a meta-analysis in Oncomine database in five sarcoma datasets. Eight network 2 genes (KIAA0101, HDAC2, SUMO1, RBBP4, NONO, RBBP7, HTRA2, and MTA2) were significantly differentially expressed in an array of 18 different sarcoma types. Finally, Gene Ontology annotation enrichment analysis revealed significant roles of the PARK7 interactome in NuRD, CHD, and SWI/SNF protein complexes. In conclusion, we identified 13 novel genes differentially expressed in MPM, never reported before. Among them, BBS1 emerged as a novel predictor of overall survival in MPM. Finally, we identified that PARK7 interactome is involved in novel pathways pertinent in MPM disease.

Characterization and comparative genomic analysis of intronless Adams with testicular gene expression

Genomics ◽  
2004 ◽  
Vol 83 (4) ◽  
pp. 636-646 ◽  
Author(s):  
Inchul Choi ◽  
Jungsu Oh ◽  
Byung-Nam Cho ◽  
Joohong Ahnn ◽  
Yong-Keun Jung ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic
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