Segmentation and intensity estimation for microarray images with saturated pixels
Ontology highlight
ABSTRACT:
ORGANISM(S): synthetic construct Homo sapiens
PROVIDER: GSE33899 | GEO | 2011/11/23
SECONDARY ACCESSION(S): PRJNA148259
REPOSITORIES: GEO
Similar Datasets
Project description:Images and gpr files were examined using a novel saturation reduction method to determine whether accuracy could be improved by extending dynamic range of saturated pixels Three immunosignatures from human Valley Fever (Coccidiodes) patients and three immunosignatures from human influenza vaccine recipients were examined to test an algorithm that extends the apparent dynamic range of a fluorescence image. These images had several saturated spots at 70PMT and 100% laser power. The program examined the differences between Valley Fever and influenza in terms of standard image processing vs. segmentation and intensity estimation.
2011-11-23 | E-GEOD-33899 | biostudies-arrayexpress
Project description:Segmentation and intensity estimation for microarray images with saturated pixels
| PRJNA148259 | ENA
Project description:BackgroundMicroarray image analysis processes scanned digital images of hybridized arrays to produce the input spot-level data for downstream analysis, so it can have a potentially large impact on those and subsequent analysis. Signal saturation is an optical effect that occurs when some pixel values for highly expressed genes or peptides exceed the upper detection threshold of the scanner software (2(16) - 1 = 65, 535 for 16-bit images). In practice, spots with a sizable number of saturated pixels are often flagged and discarded. Alternatively, the saturated values are used without adjustments for estimating spot intensities. The resulting expression data tend to be biased downwards and can distort high-level analysis that relies on these data. Hence, it is crucial to effectively correct for signal saturation.ResultsWe developed a flexible mixture model-based segmentation and spot intensity estimation procedure that accounts for saturated pixels by incorporating a censored component in the mixture model. As demonstrated with biological data and simulation, our method extends the dynamic range of expression data beyond the saturation threshold and is effective in correcting saturation-induced bias when the lost information is not tremendous. We further illustrate the impact of image processing on downstream classification, showing that the proposed method can increase diagnostic accuracy using data from a lymphoma cancer diagnosis study.ConclusionsThe presented method adjusts for signal saturation at the segmentation stage that identifies a pixel as part of the foreground, background or other. The cluster membership of a pixel can be altered versus treating saturated values as truly observed. Thus, the resulting spot intensity estimates may be more accurate than those obtained from existing methods that correct for saturation based on already segmented data. As a model-based segmentation method, our procedure is able to identify inner holes, fuzzy edges and blank spots that are common in microarray images. The approach is independent of microarray platform and applicable to both single- and dual-channel microarrays.
| S-EPMC3269438 | biostudies-literature
Project description:Intake and absorption of cholesterol (the latter determined by double labeled cholesterol methodology) were nearly unchanged in mice fed the saturated fat diet, but the fecal excretion of neutral sterols (i.e. cholesterol and its microbial conversion products) was increased compared with control diet(+80%; p<0.01). The saturated fat diet did neither significantly affect biliary cholesterol secretion nor intestinal cholesterol absorption (49% vs. 65% in controls, double labeled water methodology, p>0.1). Thus, the increased fecal neutral sterol excretion was primarily due to increased net transintestinal cholesterol excretion (+89% versus control; p<0.05). Since a major fraction of TICE cholesterol absorption is normally reabsorbed (J Lipid Res 2019 Sep;60(9):1562-1572), the increased fecal cholesterol excretion could be due to more transintestinal excretion of cholesterol into the intestinal lumen and/or to its decreased reabsorption. The saturated fat diet increased jejunal expression of genes involved in cholesterol synthesis (Srebf2 and target genes), but did not affect whole body de novo cholesterol synthesis. Conclusion This proof-of-principle study shows that increasing the saturation of the dietary fat can stimulate fecal cholesterol excretion. Individual components of saturated fat diets are to be explored to address the responsible molecular mechanisms
2021-02-01 | GSE37097 | GEO
Project description:Astrocytes are essential regulators of the central nervous systems response to disease and injury and have been hypothesized to actively kill neurons in neurodegenerative disease. There has been intense interest in identifying the putative toxic factor(s) secreted by astrocytes. Here, we report a biochemical approach to isolate the astrocyte-derived toxic factor. Unexpectedly, instead of a protein, we found saturated lipids contained in ApoE/ApoJ lipoparticles as components of astrocyte-mediated toxicity in vitro and in vivo. Eliminating the formation of long-chain saturated lipids by astrocyte cell-type-specific knockout of the saturated lipid synthesis enzyme ELOVL1 mitigates astrocyte-mediated toxicity in vitro as well as in an acute axonal injury model in vivo. These results suggest a new mechanism by which astrocytes kill cells in the CNS.
2021-07-12 | MSV000087805 | MassIVE
Project description:The phospholipid and free fatty acid (FFA) composition of neuronal membranes plays a crucial role in learning and memory, but the mechanisms through which neuronal activity affects the brain's lipid landscape remain largely unexplored. Saturated FFAs, particularly myristic acid (C14:0), strongly increase during neuronal stimulation and memory acquisition, suggesting the involvement of phospholipase A1 (PLA1) activity in synaptic plasticity. Here, we show that genetic ablation of the DDHD2 isoform of PLA1 in mice markedly reduced saturated FFAs across the brain and memory performance in reward-based learning and spatial memory models prior to the development of neuromuscular deficits. DDHD2 was shown to bind to the key synaptic protein STXBP1. Using STXBP1/2 knockout neurosecretory cells and a haploinsufficient STXBP1+/- mouse model of STXBP1 encephalopathy that is also associated with intellectual disability and motor dysfunction, we show that STXBP1 controls the targeting of DDHD2 to the plasma membrane and the generation of saturated FFAs in the brain. Our findings suggest key roles for DDHD2 and STXBP1 in the lipid metabolism underlying synaptic plasticity, learning and memory.
2024-05-22 | PXD047812 | Pride
Project description:Sample and RNA preparation: The series is composed of seventeen hybridizations for analysis of differentially expressed genes in placenta tissues from women after vaginal delivery (labouring) and after elective caesarean section (non-labouring). Total RNA extraction was performed by using the MagNa Pure Compact RNA Isolation Kit (Roche Applied Science). Labeling and hybridization: Total RNA was reverse transcribed and labeled with Cy3-attached dendrimer using the Genisphere 3DNA HS kit (Genisphere) as described in the manufacturer’s protocol. Hybridizations were carried out with a TECAN HS4800 instrument using the foramamide-based hybridization buffer from Genisphere containing 5% dextran sulphate and 0.5 microgram COT1 DNA/microgram RNA at 37°C for 23 hours. 3DNA dendrimer hybridizations were carried out in formamide-based hybridization buffer alone. Post-hybridization washes were carried out at room temperature with 2xSSC for 1 min, 0.2% SDS/2xSSC for 1 min and finally with0.2xSSC for 30 sec. Scanning, image analysis and data processing: The microarrays were scanned on an AXON 4000B scanner and images were quantified using GenePix pro 6.0 software. The background estimates were calculated using the morphological opening method. Spots that displayed a signal-to-noise ratio of less than 3 or that were significantly saturated (more than 20 % saturation among foreground pixels) were filtered out. The median was used as the averaging measure of the foreground pixels. After quality control, genes that were present in less than 50 % of the arrays were filtered out. Normalization was carried out using lowess normalization Sample labelling was balanced across the groups, presumably attenuating any dye-effect. For the purpose of finding differentially expressed genes empirical Bayes analysis, using the LIMMA package was applied. The data were analysed using a two-component linear model. The prior guess of the number of D.E genes was set to 0.01. Multiple testing was accounted for by estimating the false discovery rate. We applied the Benjamini-Hochberg procedure, as well as Storeys less conservative Q-value procedure was applied. In none of the cases were any genes significant at a reasonable (15-20% FDR) level. In summary, a 2.5-fold change in expression of any gene that was present on ≥ 8 arrays was considered significant, if the difference in fluorescence intensity between two groups reached a p-value of < 0.01. Keywords: Tissue samples of placenta from women after vaginal delivery (labouring) and after elective caesarean section (non-labouring)
2007-08-01 | GSE8375 | GEO
Project description:The regulation of membrane lipid composition is critical for cellular homeostasis. Cells are particularly sensitive to phospholipid saturation, with increased saturation causing membrane rigidification and lipotoxicity. How mammalian cells sense membrane lipid composition and reverse fatty acid (FA)-induced membrane rigidification is poorly understood. Here we systematically identify proteins that differ between mammalian cells fed saturated versus unsaturated FAs. The most differentially expressed proteins were two ER-resident polytopic membrane proteins: the E3 ubiquitin ligase RNF145 and the lipid hydrolase ADIPOR2. In unsaturated lipid membranes, RNF145 is stable, promoting its lipid-sensitive interaction, ubiquitination and degradation of ADIPOR2. When membranes become enriched in saturated FAs, RNF145 is rapidly auto-ubiquitinated and degraded, stabilising ADIPOR2, whose hydrolase activity restores lipid homeostasis and prevents lipotoxicity. We therefore identify RNF145 as a FA-responsive ubiquitin ligase which, together with ADIPOR2, define an autoregulatory pathway that controls cellular membrane lipid homeostasis and prevents acute lipotoxic stress.
2022-08-10 | PXD034835 | Pride
Project description:Gene expression pattern in murine 3T3-L1 adipocytes treated with saturated fatty acid (palmitate) in the presence or absence of PI3K p110alpha-selective inhibitor A66.
2020-01-01 | GSE129442 | GEO
Project description:Saturated Fat Impairs Circadian Transcriptomics through Histone Modification of Enhancers
| PRJNA847177 | ENA