CARMA: A platform for analyzing microarray datasets that incorporate replicate measures

Greer, Kevin; McReynolds, Matthew R.; Brooks, Heddwen L.; Hoying, James B.

doi:10.1186/1471-2105-7-149

Cited by 18 publications

(5 citation statements)

References 38 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For data processing, the bioconductor packages pipelined through R interfaces DaNTE [41] and CARMA [42] were used. Pre-processing and normalization was completed with the Affy package.…”

Section: Methodsmentioning

confidence: 99%

MicroRNA profiling of novel African American and Caucasian Prostate Cancer cell lines reveals a reciprocal regulatory relationship ofmiR-152and DNA methyltranferase 1

et al. 2014

View full text Add to dashboard Cite

miRNA expression in African American compared to Caucasian PCa patients has not been widely explored. Herein, we probed the miRNA expression profile of novel AA and CA derived prostate cancer cell lines. We found a unique miRNA signature associated with AA cell lines, independent of tumor status. Evaluation of the most differentially expressed miRNAs showed that miR-132, miR-367b, miR-410, and miR-152 were decreased in more aggressive cells, and this was reversed after treatment of the cells with 5-aza-2′-deoxycytidine. Sequencing of the miR-152 promoter confirmed that it was highly methylated. Ectopic expression of miR-152 resulted in decreased growth, migration, and invasion. Informatics analysis of a large patient cohort showed that decreased miR-152 expression correlated with increased metastasis and a decrease in biochemical recurrence free survival. Analysis of 39 prostate cancer tissues with matched controls (20 AA and 19 CA), showed that 50% of AA patients had statistically significant lower miR-152 expression compared to only 35% of CA patients. Ectopic expression of miR-152 in LNCaP, PC-3, and MDA-PCa-2b cells down-regulated DNA (cytosine-5)-methyltransferase 1 (DNMT1) through direct binding in the DNMT1 3'UTR. There appeared to be a reciprocal regulatory relationship of miR-152/DNMT1 expression, as cells treated with siRNA DNMT1 caused miR-152 to be re-expressed in all cell lines. In summary, these results demonstrate that epigenetic regulation of miR-152/DNMT1 may play an important role in multiple events that contribute to the aggressiveness of PCa tumors, with an emphasis on AA PCa patients.

show abstract

“…For data processing, the bioconductor packages pipelined through R interfaces DaNTE [41] and CARMA [42] were used. Pre-processing and normalization was completed with the Affy package.…”

Section: Methodsmentioning

confidence: 99%

MicroRNA profiling of novel African American and Caucasian Prostate Cancer cell lines reveals a reciprocal regulatory relationship ofmiR-152and DNA methyltranferase 1

et al. 2014

View full text Add to dashboard Cite

show abstract

“…RNA was reverse transcribed and amplified using SenseAmp (Genisphere) and SuperScript III (Invitrogen) and dye-coupled with Alexa Fluor 555 or Alexa Fluor 647 (Invitrogen). Sample pairs were hybridized with 70 SlideHyb Glass Array Hybridization Buffer #1 (Ambion) in a GeneTAC Hybridization Station (Genomic Solutions); slides were scanned with an Axon GenePix scanner, and the results were analyzed using the R package CARMA ( Greer et al, 2006 ). For Affymetrix microarray analysis, soleus muscle tissue was dissected ( n = 3) and stored in Ambion RNAlater (Invitrogen).…”

Section: Methodsmentioning

confidence: 99%

Removal of immunoglobulin-like domains from titin’s spring segment alters titin splicing in mouse skeletal muscle and causes myopathy

Buck

Smith

Chung

et al. 2014

Journal of General Physiology

View full text Add to dashboard Cite

show abstract

“…For each sample 750ng of cDNA (Nanodrop, Thermo scientific) from each sample was hybridized (Ambion: Slide-Hyb buffer #1) for 16 hours at 42°C after which slides were scanned at 595 nm and 685 nm with an Array WoRx scanner. Spot finding was done with SoftWoRx Tracker and spot analysis with CARMA (27). The analysis detects relative changes in the fluorescence of a probe (adult as compared to neonate).…”

Section: Methodsmentioning

confidence: 99%

“…Significance was defined using the Student’s t-test and probability values <0.05 were taken as significant and are indicated on Figures as: * p<0.05; ** p<0.01; *** p<0.001. ANOVA with a linear model that incorporates terms to account for experimental variability was used in analysis of microarray data (for details see(27)).…”

Section: Methodsmentioning

confidence: 99%

Differential splicing of the large sarcomeric protein nebulin during skeletal muscle development

Buck

Hudson

Ottenheijm

et al. 2010

Journal of Structural Biology

View full text Add to dashboard Cite

We studied differential splicing of nebulin, a giant filamentous F-actin binding protein (M r ~700-800 kDa) that is found in skeletal muscle. Nebulin spans the thin filament length, its C-terminus is anchored in the Z-disc, and its N-terminal region is located toward the thin filament pointed end. Various lines of evidence indicate that nebulin plays important roles in thin filament and Z-disc structure in skeletal muscle. In the present work we studied nebulin in a range of muscle types during postnatal development and performed transcript studies with a mouse nebulin exon microarray, developed by us, whose results were confirmed by RT-PCR. We also performed protein studies with high-resolution SDS-agarose gels and Western blots, and structural studies with electron microscopy. We found during postnatal development of the soleus muscle major changes in splicing in both the super-repeat region and the Z-disc region of nebulin; interestingly, these changes were absent in other muscle types. Three novel Z-disc exons, previously described in the mouse gene, were upregulated during postnatal development of soleus muscle and this was correlated with a significant increase in Z-disc width. These findings support the view that nebulin plays an important role in Z-disc width regulation. In summary, we discovered changes in both the super-repeat region and the Z-disc region of nebulin, that these changes are muscle-type specific, and that they correlate with differences in sarcomere structure.

show abstract

CARMA: A platform for analyzing microarray datasets that incorporate replicate measures

Cited by 18 publications

References 38 publications

MicroRNA profiling of novel African American and Caucasian Prostate Cancer cell lines reveals a reciprocal regulatory relationship ofmiR-152and DNA methyltranferase 1

MicroRNA profiling of novel African American and Caucasian Prostate Cancer cell lines reveals a reciprocal regulatory relationship ofmiR-152and DNA methyltranferase 1

Removal of immunoglobulin-like domains from titin’s spring segment alters titin splicing in mouse skeletal muscle and causes myopathy

Differential splicing of the large sarcomeric protein nebulin during skeletal muscle development

Contact Info

Product

Resources

About