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Microarray data

Tìm thấy 20+ kết quả cho từ khóa "Microarray data"

Estimation of missing values using optimised hybrid fuzzy C - means and majority vote for microarray data

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Microarray missing values imputation methods: Critical analysis review. Accounting for the multiple natures of missing values in label-free quantitative proteomics data sets to compare imputation strategies. (2010) Missing values estimation in microarray data using fuzzy clustering and semantic similarity

Transcriptomic responses to wounding: Meta-analysis of gene expression microarray data

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meta-analysis of gene expression microarray data. Results: We collected available microarray transcriptomic profiles obtained from different tissue injury experiments and selected the genes showing a minimum twofold change in expression in response to wounding in prevailing number of experiments for each of five wound healing stages we distinguished: haemostasis &.

Comprehensive investigation of the gene expression system regulated by an Aspergillus oryzae transcription factor XlnR using integrated mining of gSELEXSeq and microarray data

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Comprehensive investigation of the gene expression system regulated by an Aspergillus oryzae transcription factor XlnR using integrated mining of gSELEX- Seq and microarray data. AoXlnR is a key TF involved in the expression of xylanolytic and cellulolytic enzymes in the filamentous fungi, Aspergillus oryzae. In this study, the data from gSELEX-Seq analysis and data mining were applied toward a comprehensive investigation of the AoXlnR-regulated transcriptional network in A.

Microarray and metabolome analysis of hepatic response to fasting and subsequent refeeding in zebrafish (Danio rerio)

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Validation of the microarray gene expression data To confirm the significance of the differential mRNA ex- pression patterns observed in the microarray data, real- time PCR analysis was performed on selected genes that exhibited distinct temporal profiles during fasting and refeeding. There was also a good distinction be- tween groups, indicating differences in the metabolite contents among the different time points.

Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice

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The distribution of KEGG annotations of the up-regulated genes by Xoo in the rice microarray data.. The distribution of KEGG annotations of the down-regulated genes by Xoo in the rice microarray data.. The distribution of KEGG annotations of the up-regulated genes by Mor in the rice microarray data.. The distribution of KEGG annotations of the down-regulated genes by Mor in the rice microarray data..

The role of AKR1 family in tamoxifen resistant invasive lobular breast cancer based on data mining

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The microarray data included 12 samples, such as TAM- sensitive invasive lobular breast cancer cell line (SUM44), TAM-resistant invasive lobular breast cancer cell line (LCCTam), TAM-treated invasive lobular breast can- cer cell line (SUM44-4HT) for 24 h and TAM-deficient cell line treated for 14 d, 3 repetition was performed for each sample.

A large-scale comparative study of isoform expressions measured on four platforms

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We then combined the data with the matched RNA-seq, Exon-array, and Microarray data of 46 of the 59 cell lines for the comparative analysis..

A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells

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Similar as with the microarray data, the three repli- cates at a given temperature were generally more strongly correlated than different temperatures in case of the 3′ RNA-Seq data from S2R+ cells (Fig. 0.01) resulted in more DE genes in case of the microarray data from S2R+ cells compared to the 3′.

Cluster analysis of replicated alternative polyadenylation data using canonical correlation analysis

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Due to high labour and time costs, microarray or RNA-seq experiments are usually measured with limited number of replicates (e.g.,. To avoid the inaccuracy introduced by the small number of replicates, here we employed the shrinkage correlation coefficient (SCC) which has been applied in the analysis of replicated microarray data [33]..

HetEnc: A deep learning predictive model for multi-type biological dataset

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An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens

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The validation of the microarray and identification of DEGs related to IMF metabolism. The breast was used as the control, and comparisons between the thigh and breast at 42 d and 90 day of age were respectively performed (42BB vs 42BT, and 90BB vs 90BT), respect- ively. To validate the reliability of the microarray data, the normal distribution analysis was performed in four microarrays, and data of each microarray was in accord- ance with normal distribution (Fig.

L-lactate induces specific genome wide alterations of gene expression in cultured bovine granulosa cells

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This limits the extrapolation of the data obtained in vitro to in vivo conditions.. 2 Validation of the microarray data from selected marker genes of the folliculo-luteal transition with quantitative real-time PCR. a PCA of the qPCR data showed highest variation between L-lactate treated and both control groups. NaCl treated cells revealed similar fold changes in the microarray and qPCR dataset. NaCl vehicle control). HAS2 hyaluronan synthase E-07 2.70E-05.

Transcriptional profiling and pathway analysis reveal differences in pituitary gland function, morphology, and vascularization in chickens genetically selected for high or low body weight

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Data from the microarray analysis were processed, normalized, and trimmed as described earlier using software that is part of the TM4 suite of microarray data analysis applications [74] freely available from The Institute for Genomic Research (TIGR, Rock- ville, MD). 90% of the lowest median pixel intensity for the salmon DNA control spots (back- ground. 8 spots/slide) among all slides were also elimi- nated from further consideration, as were any spots that were not detectable on at least half of

Data Mining and Knowledge Discovery Handbook, 2 Edition part 129

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In conclusion, SAS Enterprise Miner, Megaputer PolyAnalyst, PASW, and IBM Intelligent Miner offer the greatest diversification of data mining algorithms.. This chapter has discussed commercial data mining software that is applicable to super- computing for 3-D visualization and very large microarray databases.

A transcriptional landscape of 28 porcine tissues obtained by super deepSAGE sequencing

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The Super deepSAGE reduced cost by multiplexing and obtained data with good quality in terms of sequencing depth, gene coverage, and reprodu- cibility. Few discrepancies were observed when compar- ing Super deepSAGE data with published microarray data.

Managing and Mining Graph Data part 57

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NeMo is ap- plied on 105 human microarray datasets and recurrent co-expression clusters are identified. Functional homogeneity of these clusters are validated based on ChIP-chip data and conserved motif data [115].. The information contained in 𝑎𝑡𝑡𝑟(𝐴 𝑖 , 𝐴 𝑗 ) vary depending on the resolution of the structure. 𝐴 𝑘 , where 𝐴 𝑖 is the 𝑖 𝑡ℎ atom and 𝑆 is the set of mining bonds describing this struc- ture.

Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest

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available Affymetrix® GeneChip® data sets based on functional regions of interest. One main drawback to microarray data analysis involves the selection of probes to represent a specific transcript of interest, particularly in light of the fact that transcript-specific knowledge (notably alternative splicing) is dynamic in nature.. technology based on functional regions of interest.

Candidate gene prioritization for chronic obstructive pulmonary disease using expression information in protein–protein interaction networks

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Moreover, to further exhibit the effectiveness and robustness of the PEP method, it was applied to another independent microarray data, GSE76925 from the GEO database, which contained 40 normal samples and 111. Parameters of the PEP method Optimal value of parameter h.

A deficiency in SUMOylation activity disrupts multiple pathways leading to neural tube and heart defects in Xenopus embryos

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In order to validate the microarray data, the same RNA samples were used for qRT-PCR assays of genes selected based upon either the magnitude of the change in expression (dmrta1, rpl8, ccng1), the occurrence of the gene in a pathway involved in patterning the early embryo (xbra, foxc1, wnt8b, gsc, chrd), or a previous microarray analysis of X. (A graphical comparison of the micro- array and qRT-PCR data is presented in Additional file 3:.

Overlapping and unique roles played by ROCK1 and 2 in the modulation of coding and long noncoding RNA expression

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The verification of the microarray data was performed using 11 mRNAs and 9 lncRNAs that were possibly in- volved in ROCK signaling according to the bioinformatics analysis. microarray was listed in the brackets following each verified gene. The results of the qRT-PCR analysis (Fig. Rho-kinases are direct downstream effectors of Rho guano- sine triphosphatases, which participate in the regulation of cytoskeletal reorganization and motility.