Journal: BMC Bioinformatics

Article Title: GATExplorer: Genomic and Transcriptomic Explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs

doi: 10.1186/1471-2105-11-221

Figure Lengend Snippet: Comparison of the differential expression calculated by the SAM algorithm for a series of data of mouse microarrays (five sets of six samples) analyzed using three different expression signal calculation algorithms (MAS5.0, FARMS and RMA) with standard CDFs to "probesets" or using RMA with CDFs to "genes" ( GeneMapper CDFs) . Each set includes three biological replicates of knock-out (KO) mice for a specific gene compared to three replicates of the corresponding wild-type (WT) mice. The gene KOs are: APOE-/-, IRS2-/-, NRAS-/-, SCD1-/- and ENG+/-. The full name of these genes, the Ensembl ID number (ENSG) and the probesets assigned by Affymetrix are indicated in the top line of each set, labelled Entry (1) . The table shows the numbers for the statistical parameters calculated in the comparison, which are: (2) rank of the KO gene across down-regulated genes; (3) rank of the KO gene across all genes; (4) p-value from SAM for the KO gene; (5) d-value from SAM for the KO gene; (6) number of significant gene loci with q-value < 0.10 (this calculation was performed such that all probesets were assigned to specific genes following the Affymetrix assignment or the GeneMapper assignment; therefore the methods are comparable since the number of gene loci indicated are the fraction of total mouse genes assigned); (7) total number of mouse gene loci assigned within the microarray; (8) percentage of significant gene loci with respect to the total. Yellow background indicates the top values for each statistical parameter calculated with each of the four procedures used. The comparison that includes the identical methods for expression calculation ( RMA ) and for differential expression ( SAM ) changing only the CDFs is presented in the last two columns, framed with a black line.

Article Snippet: BLASTN sequence alignment was used to map the 25-mer oligo probes of the main Affymetrix expression microarrays to the RNA sequences of human, mouse and rat, selecting only complete perfect match alignments.

Techniques: Expressing, Knock-Out, Microarray

Journal: Nucleic Acids Research

Article Title: Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

doi: 10.1093/nar/gks1358

Figure Lengend Snippet: Reactions associated with hybridization of nucleic acids strands

Article Snippet: For instance, 25-mer probes on the Agilent microarray respond with a power curve, i.e. Freundlich isotherm y = ax b ( , panel A).

Techniques: Hybridization, Microarray

Journal: Nucleic Acids Research

Article Title: Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

doi: 10.1093/nar/gks1358

Figure Lengend Snippet: Comparison of experimental data (filled symbols) and expected isotherm (dashed line). In this plot, I is the measured fluorescence intensities from the microarray spots, while ΔΔG is the hybridization free energy as obtained from the nearest-neighbor model measured with respect to the PM free energy, for which ΔΔG = 0. The experiments are obtained from an Agilent custom array [for more details see ].

Article Snippet: For instance, 25-mer probes on the Agilent microarray respond with a power curve, i.e. Freundlich isotherm y = ax b ( , panel A).

Techniques: Fluorescence, Microarray, Hybridization

Journal: Nucleic Acids Research

Article Title: Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

doi: 10.1093/nar/gks1358

Figure Lengend Snippet: ToF-SIMS images of the P ion in single printed DNA spots show large variability of DNA concentration in and across the microarray spots. Spots are printed from 20 and 40 μM DNA concentration drops (from left to right) with 100% of the DNA tagged with Cy3. Image size (400 × 400 μm). The Cy3 fluorescence images of the same spots are shown for comparison.

Article Snippet: For instance, 25-mer probes on the Agilent microarray respond with a power curve, i.e. Freundlich isotherm y = ax b ( , panel A).

Techniques: Concentration Assay, Microarray, Fluorescence

Journal: Bioinformatics

Article Title: PatMaN: rapid alignment of short sequences to large databases

doi: 10.1093/bioinformatics/btn223

Figure Lengend Snippet: HGU95-A probes and Bonobo Reads against Chromosome 22

Article Snippet: We used PatMaN to match 201 807 Affymetrix HGU95-A microarray 25mer probes to the chimpanzee genome (panTro2).

Techniques:

Journal: BMC Bioinformatics

Article Title: Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

doi: 10.1186/1471-2105-10-77

Figure Lengend Snippet: Classification of the 604,258 probes within the Affymetrix U133Plus2 microarray . The pie chart depicts the relative percentage of probes comprising each of the nine probe categories described in the Methods section.

Article Snippet: The Human Genome U133Plus2 microarray (Affymetrix) contains 604,258 perfect match (PM) 25 mer probes organized into 54,675 probe sets which interrogate the relative abundance of ~47,000 human transcripts.

Techniques: Microarray

Journal: BMC Bioinformatics

Article Title: Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

doi: 10.1186/1471-2105-10-77

Figure Lengend Snippet: Classification of the 54,675 probe sets within the Affymetrix U133Plus2 microarray . The composition of probe sets with respect to probe categories is depicted. The height of each bar represents the number of probe sets (Y-axis) that contain a least one probe in the indicated category (X-axis). The gray segment of each bar represents the number of probe sets where less than six probes of the indicated category are present. The black segment comprising each bar represents the number of probe sets where more than six probes of the indicated category are present.

Article Snippet: The Human Genome U133Plus2 microarray (Affymetrix) contains 604,258 perfect match (PM) 25 mer probes organized into 54,675 probe sets which interrogate the relative abundance of ~47,000 human transcripts.

Techniques: Microarray

Journal: BMC Bioinformatics

Article Title: Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees

doi: 10.1186/1471-2105-10-77

Figure Lengend Snippet: Classification of probes in the Affymetrix U133Plus2 microarray

Article Snippet: The Human Genome U133Plus2 microarray (Affymetrix) contains 604,258 perfect match (PM) 25 mer probes organized into 54,675 probe sets which interrogate the relative abundance of ~47,000 human transcripts.

Techniques: