microarray processing and data analysis  (Genome Explorations)

Journal: BMC Bioinformatics

Article Title: Workflows for microarray data processing in the Kepler environment

doi: 10.1186/1471-2105-13-102

Figure Lengend Snippet: Microarray Workflow Listing

Article Snippet: In the Taverna system, there are a number of related workflows for Affymetrix microarray data processing [ ].

Techniques: Microarray, Modification, Binding Assay, Expressing, Variant Assay

Journal: BMC Bioinformatics

Article Title: Workflows for microarray data processing in the Kepler environment

doi: 10.1186/1471-2105-13-102

Figure Lengend Snippet: Screenshot of a simple Kepler workflow for calculating statistics of the “ratio” column of microarray GFF files . Python (Jython) and R implementation. Note that red arrows and italicized red text are not part of original screen view but are added to show basic parts of a Kepler workflow screen. All other text is part of screenshot. See RESULTS for details.

Article Snippet: In the Taverna system, there are a number of related workflows for Affymetrix microarray data processing [ ].

Techniques: Microarray

Journal: BMC Bioinformatics

Article Title: Workflows for microarray data processing in the Kepler environment

doi: 10.1186/1471-2105-13-102

Figure Lengend Snippet: A full Affymetrix gene expression microarray analysis workflow in Kepler. This workflow uses well-established R/BioConductor modules following the steps recommended in a published pipeline . Several resulting graphs and files are output. See RESULTS for details.

Article Snippet: In the Taverna system, there are a number of related workflows for Affymetrix microarray data processing [ ].

Techniques: Expressing, Microarray

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Map position of eQTL . Genetic position of the significant eQTL associations found in biological replicate 1. Genetic position of SNP marker (cM by chromosome) most significantly associated with the differential transcript abundance, x-axis. Genetic position of gene being measured by unique microarray probe, y-axis. The most significant associations (blue, KS p-value ≤ 1E -15 ) generally function in cis (diagonal line) where the eQTL and the transcript being measured map to the same genetic position. The weaker associations (pink, KS p-value ≥ 10 -15 ) generally function in trans (periphery) where the eQTL maps to a position other than the transcript being measured.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Marker, Microarray

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Quantity and mode of action of eQTL . eQTL were categorized as cis- or trans-acting based on map positions of the eQTL as compared to the genomic origin of the gene being measured by the microarray. A total of 10,941 eQTL were identified that were analyzable for mode of action based on strict transcript genomic origin criteria. Ninety per cent of all eQTL (9,795 of 10,941) functioned through a cis regulatory mechanism. Normalizing the number of eQTL identified as cis- or trans-shows that the stronger eQTL tend to function through cis-regulation (red, n = 9,795) while weaker eQTL tend to function through trans-regulation (blue, n = 1,146).

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Microarray

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: False positive cis-eQTL . Relative expression levels determined by the microarray suggests that cis-acting factors regulate the expression of two example genes. In both cases (A,B) the B73 transcript abundance is far greater than that of Mo17 according to the microarray. Amplification of genomic and cDNA sequence from B73 and Mo17 reveals that actual expression in situ may be more similar than the microarray would suggest. Sequence analysis of the probe-hybridization loci reveal that the microarray probes (red highlight) would fail to hybridize efficiently to the Mo17 alleles, thus inappropriately suggesting extreme differential expression and strong cis-eQTL. Blue boxes show polymorphisms between the Mo17-derived sequences as compared to the reference probe and B73-derived sequences.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Expressing, Microarray, Amplification, Sequencing, In Situ, Hybridization, Derivative Assay

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Sequence gap in the physical map masks probe homology sites . A Schematic of selected maize chromosomes. A "master regulating" trans-eQTL residing on chromosome 2, BAC AC207404 (blue diamond) regulates expression of two iron superoxide dismutase genes on the long arms of chromosomes 1 (BAC AC221053) and 6 (BAC AC187242), as measured by unique microarray probes (red and cyan, respectively); centromeres = black circles . B Re-sequencing analysis of the eQTL interval on chromosome 2 revealed a 2 kb gap (gray dotted line) in the known sequence (gray bars). Probe homology sites for both regulated genes were discovered within the gap negating a trans-acting master regulator effect, therefore suggesting a strong cis-acting eQTL in the vicinity of the newly identified third iron superoxide dismutase gene.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Sequencing, Expressing, Microarray

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Fine mapping of eQTL regulating ABA 8'-hydroxylase . A Microarray expression data revealed greater expression of the target gene ABA 8'-hydroxylase. The target gene is present in both parental backgrounds but is much more strongly expressed under control of a B73 derived allele of the trans-regulator glutamine amidotransferase. Multiple splice variants are amplified from the pseudogene cDNA. Sequence analysis of variants shows that only the smallest band is able to hybridize to the microarray probe, asterisk . Among parental controls, the B73 inbred average expression shows a 9-fold greater expression of the pseudogene as compared the Mo17 inbred. An F1 hybrid shows mid-level expression regulation of the relevant band, asterisk , as well as several others. B Example phenotypes/genotypes found within the IBM2 Syn10 population and controls. Phenotypes are considered "high" or "low" depending on the relative ABA 8'hydroxylase target gene expression levels. B73 alleles of the eQTL allow for high expression of the target as compared to Mo17 alleles; B73 derived allele = green, Mo17 derived allele = blue. Fine mapping of the IBM2 Syn10 population using molecular markers (M1-M6) identified a very small region at the 3' end of the gene as being the responsible element that determines the expression of the target. C BACs within eQTL interval with public markers (IDP markers; red) and designed mapping markers M1-M6 (teal) spanning the region (not drawn to scale). IDP3798 and two mapping markers are located within the glutamine amidotransferase gene.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Microarray, Expressing, Derivative Assay, Amplification, Sequencing

Journal: BMC Genomics

Article Title: Genome-wide expression quantitative trait loci (eQTL) analysis in maize

doi: 10.1186/1471-2164-12-336

Figure Lengend Snippet: Unexpected expression regulation of a pseudogene results from sequence variation in the carboxy terminal of glutamine amidotransferase . A The B73 and Mo17derived sequences for the trans-regulator glutamine amidotransferase code for nearly identical proteins. Blue boxes highlight residues different from the B73 reference sequence. Fine mapping of the eQTL to a 186 bp interval determined that the carboxy-terminus accounts for the trans-regulation, black bar . Class I glutamine amidotransferase proteins require the conserved C-H-E triad (red boxes) for their expected enzymatic functions suggesting that, despite the sequence differences between the genotypes, the proteins likely remain functional in their expected pathway in situ. B Genomic structure on chromosome 1(BAC AC177817) that encodes for the pseudogene is derived from chimerization of 1.5 exons of the functional ABA 8'-hydroxylase genic region (blue bar, blue exons) of chromosome 4 (BAC AC182187), a 5' element enabling transcription originating from chromosome 10 (green bar; BAC AC194847), and genomically non-unique sequence (yellow dashed bar, yellow exons). The microarray probe (red bar) used to measure the pseudogene is unique within the transcriptome.

Article Snippet: The Agilent microarray expression data (raw and processed) are available from GEO (Series Accession GSE29964).

Techniques: Expressing, Sequencing, Functional Assay, In Situ, Derivative Assay, Microarray