Gender dependent expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE3778 | GEO | 2006/12/31
SECONDARY ACCESSION(S): PRJNA93969
REPOSITORIES: GEO
Similar Datasets
Project description:Gender dependent gene expression in the kidney of 36 day old rats using the Affymetrix GeneChip rat expression set 230 array RAE230A. mixed model ANOVA using log2 transformed signal intensity of PM. Keywords: repeat Three rat strains Mhm, Us and MhmBN were examined. Three arrays were performed for each gender and strain combination. Total RNA from three rats was pooled for each array.
2010-06-05 | E-GEOD-3778 | biostudies-arrayexpress
Project description:Copy number profiling of 36 ovarian tumors on Affymetrix 100K SNP arrays Thirty-six ovarian tumors were profiled for copy-number alterations with the Affymetrix 100K Mapping Array. Copy number profiling of 36 ovarian tumors on Affymetrix 500K SNP arrays Sixteen ovary tumors were profiled for copy-number alterations with the high-resolution Affymetrix 500K Mapping Array. Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1). Affymetrix 500K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization. Forty-eight normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=500k) and analyzed at the same time. One CEL file for each set (Sty and Nsp) with the median signal intensity across the set was selected as the reference array. The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows. For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set. For Chromosome X, the average of the 20 normal female samples was used. Each probe set was mapped to the genome, NCBI assembly version 36, using annotation provided by the Affymetrix web site. The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment. Copy number was calculated as power(2,log2ratio + 1).
2010-12-16 | E-GEOD-26075 | biostudies-arrayexpress
Project description:The immunological reaction to exercise has been investigated with increasing intensity in the last 10-20 years, with most human studies performed in male subjects. Recently, gender-specific aspects have received growing attention, but studies carefully monitoring the influence of gender, including the menstrual cycle, are rare. Here, we report gene expression patterns in response to a run at 93% of the individual anaerobic threshold of 9 women with regular menstrual cycles and no use of oral contraceptives who ran both at day 10 (follicular phase, F) and at day 25 (luteal phase, L) of their cycle. 12 male subjects (M) served as controls. The mRNA was pooled group wise and processed on a gene expression microarray encompassing 789 genes, including major genes of the inflammatory and anti-inflammatory reaction. The differences of gene expression between time points t0 (before run) and t1 (after run) were analyzed. Females in L showed a higher extent of regulation than females in F or men. Among those genes which were up-regulated above 1.5 fold change (log2), pro-inflammatory genes were significantly enriched (p=0.033, after Bonferroni correction) in L, while this was not the case in F or M. Conversely, women in L showed a strong trend towards down-regulation of anti-inflammatory genes. Some prominent genes like interleukin (IL)-6 and IL1RN (coding for IL-1 receptor antagonist, also used as IL1RA) were clearly regulated in opposite directions in L as opposed to F and M. In conclusion, women in L showed a distinctly different pattern of gene regulation in response to exercise, compared with women in F or M. The overall direction of gene expression changes of women in L is clearly pro-inflammatory. This finding accentuates a need for careful consideration of the female cyclic phase when investigating women in exercise immunology studies. Our results may also have implications relevant to other forms of stress in females. Keywords: time course, stress response
2009-02-25 | GSE14977 | GEO
Project description:Development of a clinically relevant animal models of RCC for preclinical investigations. For DNA copy number analysis, the Sty I (250K) SNP array of the 500K Human Mapping Array (Affymetrix) was used. Arrays were scanned by GeneChip Scanner 3000 7G. Probe-level signal intensities were normalized to a baseline array with median intensity using invariant set normalization and SNP-level signal intensities were obtained using a model-based (PM/MM) method. Keywords: SNP array data, renal cell carcinoma
2011-05-05 | GSE29062 | GEO
Project description:This study aim to understand the role of retrotransposable elements in myelination Raw data with accession number GSE11218 and GSE5940 (using Affymetrix expresion GeneChIP Rat Genome 230 2.0 and 230A, respectively) were extracted fromm GEO. Probe level information was extracted using R library rat2302probe (for Rat genome 230 2.0) and rae230aprobe (for rat genome 230A). Unique probe sequence in 230 2.0 and 230A platform were retained and the intersect probes (90507 in number) between two platforms were used for analysis. Background subtracted raw data were quantile normalized. Probes for which intensity were greater than. sample median level in at least half the arrays for one experimental condition in. a dataset were considered present; absent probes were removed. Further differentially expressed probbes between OL and OPC were identified by using R Bioconductor package 'limma'. P-values were adjusted to correct for multiple testing using FDR (Benjamini-Hochberg). Probes for which the difference between groups were > or = 2 fold and the adjusted P-value<0.05 were considered differentially expressed.
2024-02-14 | GSE245032 | GEO
Project description:Plasmodium yoelii gender-specific gametocyte transcriptome
| PRJNA923669 | ENA
Project description:Previous studies suggest that there may be age and gender related differences in salivary gland function. However, the limited and often conflicting information available from healthy populations makes it difficult to confirm these differences. The purpose of the present study was to evaluate and compare changes in gene expression associated with age and gender in the human parotid gland. Differential expression, defined as statistically significant differences with at least 1.5 fold changes, was detected using the Affymetrix® GeneChip® HGU133plus2.0 microarray in 787 gene probe sets; 320 showed higher expression in males, while 467 showed higher expression in females. Several genes associated with saliva secretion were differentially expressed in male and female parotid gland including vesicle-associated membrane protein 3 VAMP3, synaptosomal-associated protein SNAP23, RAS oncogene family member RAB1A, syntaxin binding protein STXBP1. When the gene expression results from the youngest (19-38 years old) and the oldest (65-69 years old) female subjects were further evaluated, it was found that the expression of 228 genes were altered during aging; 155 genes were down-regulated, whereas 73 genes were up-regulated in the female parotid gland. Of the genes that were altered during aging, 24 of the 28 genes (86%) classified as being associated with immune responses were down-regulated in the aged parotid gland. A panel of differentially expressed, age- and gender-related genes was selected for further study by quantitative, real-time RT-PCR. Comparable differences in gene expression were detected by both Affymetrix array and quantitative, real-time RT-PCR methods. Taken together, our data suggest that salivary gland function may be adversely affected in the aged population due, at least in part, to the down regulation of several categories of genes. Moreover, the gender specific gene expressions identified in the present study correlates with the previously observed sexual dimorphism in salivary gland function. Keywords: Human Parotid Gland
2008-12-21 | GSE8764 | GEO
Project description:Gender susceptibility to ventilator-induced lung injury
| PRJNA497744 | ENA
Project description:Transcriptional profiling of adult males and females of the lymphatic dwelling filarial parasite Brugia malayi Keywords: Gender based transcripts, filaria
2010-12-30 | GSE12944 | GEO
Project description:Gender bias and the role of sex hormones in autoimmune diseases are well established. In specific-pathogen free (SPF) non-obese diabetic (NOD) mice females have 1.3-4.4 times higher incidence of Type 1 diabetes (T1D). Germ-free (GF) mice lose the gender bias (female/male ratio 1.1-1.2). Gut microbiota differed in males and females, a trend reversed by male castration, confirming that androgens influence gut microbiota. Colonization of GF NOD mice with defined microbiota revealed that some but not all lineages overrepresented in male mice supported a gender bias in T1D, and protection did not correlate with androgen levels. However, hormone-supported selective microbial lineage variation may work as a positive feedback mechanism contributing to the sexual dimorphism of autoimmune diseases. Gene expression analysis suggested pathways involved in protection of males from T1D by microbiota.
2013-08-02 | GSE49467 | GEO