Mus musculus
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ABSTRACT:
PROVIDER: PRJNA233618 | ENA |
REPOSITORIES: ENA
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Project description:We developed a systematic statistical method, tTREAT, to identify differentially expressed genes with respect to a predefined FC threshold. The tTREAT approach aims to reduce false discoveries. We applied statistical tests relative to a Fold Change threshold to a dataset about mouse odorant receptor gene expression generated by the NanoString technology. We used mouse strains M-bM-^HM-^FP and M-bM-^HM-^FH that lack the P element and the H element respectively. We also used a mouse strain generated by chromosome engineering (M-bM-^HM-^FOlfr7M-bM-^HM-^F) whereby a 2.4 Mb region is deleted, thus lacking 99 odorant receptor genes. We sought to understand the regulation of the expression of odorant receptor genes by comparing mutant mice to wildtype mice.
2014-01-08 | E-GEOD-53876 | biostudies-arrayexpress
Project description:A total of 5762.0 proteins were identified in this study, of which 4891.0 proteins contained quantitative information. If a 1.2-fold differential expression change threshold is used and a statistical test t-test p-value < 0.05 is used as the significance threshold, then among the proteins quantified, we found that 95 proteins were up-regulated and 45 proteins were down-regulated in the treatvscontrol comparison group.
2023-05-10 | PXD040967 | Pride
Project description:To investigate the effect of ATP2 knockdown on the protein expression of Candida albicans, we performed proteomic assays for atp2Δ/Δ and wild type strains. A total of 4000.0 proteins were identified in this study, of which 3652.0 proteins contained quantitative information. If a 1.5-fold differential expression change threshold and a statistical test t-test p-value < 0.05 were used as the significance threshold, then among the quantified proteins, we found that 112 proteins were up-regulated and 268 proteins were down-regulated in atp2Δ/Δ cells. Based on the above data, we performed systematic bioinformatics analysis (protein functional annotation) of all identified proteins, and performed functional classification, functional enrichment and functional enrichment-based clustering analysis of all differentially expressed proteins.
2021-09-10 | PXD024039 | Pride
Project description:Olfactory sensory neurons express just one out of a possible ~1000 odorant receptor genes, reflecting an exquisite mode of gene regulation. In one model, once an odorant receptor is chosen for expression, other receptor genes are suppressed by a negative feedback mechanism, ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure, however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover, we show that signaling through G protein M-NM-2M-NM-3 subunits is both necessary and sufficient to suppress the expression of odorant receptor genes, and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron. Total 6 samples were analyzed-3 controls & 3 samples
2013-12-16 | E-GEOD-53334 | biostudies-arrayexpress
Project description:The goal of this study is to identify unique miRNA profiles of EVs from MCF7 and MCF10A cells that distinguish their cellular origin. 654 human mature miRNAs were analyzed in NanoString assays to identify miRNA with high abundance in MCF7 EVs and the greatest fold change for MCF7 EVs relative to MCF10A EVs.
2015-02-21 | E-GEOD-66165 | biostudies-arrayexpress
Project description:Olfactory sensory neurons express just one out of a possible ~1000 odorant receptor genes, reflecting an exquisite mode of gene regulation. In one model, once an odorant receptor is chosen for expression, other receptor genes are suppressed by a negative feedback mechanism, ensuring a stable functional identity of the sensory neuron for the lifetime of the cell. The signal transduction mechanism subserving odorant receptor gene silencing remains obscure, however. Here we demonstrate in the zebrafish that odorant receptor gene silencing is dependent on receptor activity. Moreover, we show that signaling through G protein βγ subunits is both necessary and sufficient to suppress the expression of odorant receptor genes, and likely acts through histone methylation to maintain the silenced odorant receptor genes in transcriptionally inactive heterochromatin. These results provide new insights linking receptor activity with the epigenetic mechanisms responsible for ensuring the expression of one odorant receptor per olfactory sensory neuron.
2013-12-16 | GSE53334 | GEO
Project description:Global transcriptome analysis showed that human lymphatic endothelial cells (LECs) grown on a soft matrix exhibit increased GATA2 expression, concomitant with a GATA2-dependent upregulation of genes involved in cell migration and lymphangiogenesis, including the key lymphangiogenic growth factor receptor VEGFR3. Affymetrix GeneChip analysis revealed regulation of 2771 transcripts above or below a 1.4-fold change (log2 fold change >0.5 or <-0.5) threshold on soft versus stiff matrices. Moreover, 406 (27%) of the 1485 transcripts that were increased and 207 (16 %) of the 1286 transcripts that were decreased on soft matrix were regulated in a GATA2 dependent manner.
2018-04-17 | GSE110726 | GEO
Project description:Transcriptome were compared between lenvatinib-treated and untreated C2C12 cells. 145 up-regulated genes and 285 down-regulated genes were identified by setting a 2-fold change and p < 0.05 threshold.
2024-04-15 | GSE249627 | GEO
Project description:Compared to wild type plants, overexpression of NROB results leaf early senescence, biomass and seeds yield decreased more than 70%. Microarray analysis the differential expression genes induced by NROB Young leaves of DAG 30 were harvested from WT and 35S: NROB #2 plants and frozen immediately in liquid nitrogen. Total RNA was extracted using the RNeasy plant mini kit (Qiagen) and was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100. Qualified and purified total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, Two-Color (Agilent technologies, US). Regulated genes were identified with a stringent significance threshold, namely a mean >2.0-fold change (transformants relative to WT control samples) and based on at least two replicates. Microarray analysis result was verified by real-time PCR
2015-07-01 | E-GEOD-65460 | biostudies-arrayexpress
Project description:Background Many microarray experiments search for genes with differential expression between a common “reference” group and multiple test groups, like in the case of time-course designs or of various treatments versus a control condition. In such cases, currently employed statistical approaches based on t-test or close derivatives have limited efficacy, mostly because estimation of noise is done on only two groups at time. Alternative approaches based on ANOVA correctly capture noise from all the groups, but then do not confront single test groups with the reference. We therefore conceived a statistical test for pairwise comparisons between the reference group and each test group that uses within-group variance calculated from all the groups. Results We implemented an R-Bioconductor package named Mulcom, with a statistical test derived from the Dunnett’s test, designed to compare multiple experimental groups against a common reference. In addition to the basic Dunnett’s t value, the package includes an optional minimal fold-change threshold, m. Thanks to automated, permutation-based estimation of False Discovery Rate (FDR), the package also permits fast optimization of the test, to obtain the maximum number of significant genes at a given FDR value. When applied on a time-course experiment profiled in parallel on two microarray platforms, and compared with currently used tests, Mulcom displayed higher concordance of significant genes in the two array platforms, and higher enrichment in functional annotation to categories related to the biology of the experiment. Conclusions The Mulcom package provides a fast and powerful tool for the identification of differentially expressed genes when several experimental conditions are compared with a common reference. We found that Mulcom leads to lists of differentially expressed genes that are particularly consistent across microarray platforms and enriched in significant classes of genes. In our opinion, the main reasons for these good performances are three: (i) within-group variability is estimated from all experimental groups even if only two of them are compared each time; (ii) the optional fold-change threshold m avoids false positives due to aberrantly low within-group variability; (iii) automated test optimization allows maximizing sensitivity without compromising specificity.
2011-08-10 | GSE26735 | GEO