Phase-independent rhythmic analysis of genome-wide expression patterns

2002 ◽  
Author(s):  
Christopher James Langmead ◽  
Anthony K. Yan ◽  
C. Robertson McClung ◽  
Bruce Randall Donald
Keyword(s):  
Expression Patterns ◽  
Genome Wide ◽  
Genome Wide Expression

scholarly journals Genome-wide expression patterns of invasion front, inner tumor mass and surrounding normal epithelium of colorectal tumors

2007 ◽  
Vol 6 (1) ◽  
pp. 79 ◽  
Author(s):  
Eike Staub ◽  
Joern Groene ◽  
Maya Heinze ◽  
Detlev Mennerich ◽  
Stefan Roepcke ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Colorectal Tumors ◽  
Normal Epithelium ◽  
Tumor Mass ◽  
Invasion Front ◽  
Genome Wide ◽  
Genome Wide Expression

scholarly journals Coping with Polychlorinated Biphenyl (PCB) Toxicity: Physiological and Genome-Wide Responses of Burkholderia xenovorans LB400 to PCB-Mediated Stress

2006 ◽  
Vol 72 (10) ◽  
pp. 6607-6614 ◽  
Author(s):  
J. Jacob Parnell ◽  
Joonhong Park ◽  
Vincent Denef ◽  
Tamara Tsoi ◽  
Syed Hashsham ◽  
...  
Keyword(s):  
Protein Function ◽  
Polychlorinated Biphenyl ◽  
Membrane Separation ◽  
Expression Patterns ◽  
Burkholderia Xenovorans ◽  
Inhibition Of Growth ◽  
Burkholderia Xenovorans Lb400 ◽  
Genome Wide ◽  
Differential Gene ◽  
Genome Wide Expression

ABSTRACT The biodegradation of polychlorinated biphenyls (PCBs) relies on the ability of aerobic microorganisms such as Burkholderia xenovorans sp. LB400 to tolerate two potential modes of toxicity presented by PCB degradation: passive toxicity, as hydrophobic PCBs potentially disrupt membrane and protein function, and degradation-dependent toxicity from intermediates of incomplete degradation. We monitored the physiological characteristics and genome-wide expression patterns of LB400 in response to the presence of Aroclor 1242 (500 ppm) under low expression of the structural biphenyl pathway (succinate and benzoate growth) and under induction by biphenyl. We found no inhibition of growth or change in fatty acid profile due to PCBs under nondegrading conditions. Moreover, we observed no differential gene expression due to PCBs themselves. However, PCBs did have a slight effect on the biosurface area of LB400 cells and caused slight membrane separation. Upon activation of the biphenyl pathway, we found growth inhibition from PCBs beginning after exponential-phase growth suggestive of the accumulation of toxic compounds. Genome-wide expression profiling revealed 47 differentially expressed genes (0.56% of all genes) under these conditions. The biphenyl and catechol pathways were induced as expected, but the quinoprotein methanol metabolic pathway and a putative chloroacetaldehyde dehydrogenase were also highly expressed. As the latter protein is essential to conversion of toxic metabolites in dichloroethane degradation, it may play a similar role in the degradation of chlorinated aliphatic compounds resulting from PCB degradation.

scholarly journals Meta-analysis of genome-wide expression patterns associated with behavioral maturation in honey bees

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 503 ◽  
Author(s):  
Heather A Adams ◽  
Bruce R Southey ◽  
Gene E Robinson ◽  
Sandra L Rodriguez-Zas
Keyword(s):  
Honey Bees ◽  
Meta Analysis ◽  
Expression Patterns ◽  
Genome Wide ◽  
Behavioral Maturation ◽  
Genome Wide Expression

scholarly journals Genome-wide expression patterns associated with oncogenesis and sarcomatous transdifferentation of cholangiocarcinoma

BMC Cancer ◽  
2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Min-A Seol ◽  
In-Sun Chu ◽  
Mi-Jin Lee ◽  
Goung-Ran Yu ◽  
Xiang-Dan Cui ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Genome Wide ◽  
Genome Wide Expression

scholarly journals Genome-wide Expression Analyses ofCampylobacter jejuniNCTC11168 Reveals Coordinate Regulation of Motility and Virulence byflhA

2004 ◽  
Vol 279 (19) ◽  
pp. 20327-20338 ◽  
Author(s):  
Catherine D. Carrillo ◽  
Eduardo Taboada ◽  
John H. E. Nash ◽  
Patricia Lanthier ◽  
John Kelly ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Dna Microarrays ◽  
Expression Patterns ◽  
Regulatory System ◽  
Toxin Production ◽  
Gene Encoding ◽  
Coordinate Regulation ◽  
Genome Wide ◽  
Transcript Profiles ◽  
Genome Wide Expression

We examined two variants of the genome-sequenced strain,Campylobacter jejuniNCTC11168, which show marked differences in their virulence properties including colonization of poultry, invasion of Caco-2 cells, and motility. Transcript profiles obtained from whole genome DNA microarrays and proteome analyses demonstrated that these differences are reflected in late flagellar structural components and in virulence factors including those involved in flagellar glycosylation and cytolethal distending toxin production. We identified putative σ28and σ54promoters for many of the affected genes and found that greater differences in expression were observed for σ28-controlled genes. Inactivation of the gene encoding σ28,fliA, resulted in an unexpected increase in transcripts with σ54promoters, as well as decreased transcription of σ28-regulated genes. This was unlike the transcription profile observed for the attenuatedC. jejunivariant, suggesting that the reduced virulence of this organism was not entirely due to impaired function of σ28. However, inactivation offlhA, an important component of the flagellar export apparatus, resulted in expression patterns similar to that of the attenuated variant. These findings indicate that the flagellar regulatory system plays an important role in campylobacter pathogenesis and thatflhAis a key element involved in the coordinate regulation of late flagellar genes and of virulence factors inC. jejuni.

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