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:

Article Title: Genomic Analysis of Anti-Hepatitis B Virus (HBV) Activity by Small Interfering RNA and Lamivudine in Stable HBV-Producing Cells

doi: 10.1128/JVI.79.22.14392-14403.2005

Figure Lengend Snippet: The fidelity and reproducibility of microarray profiling. (A) The CapitalBio's long oligonucleotide (Operon 70-mer) microarray and Affymetrix's short oligonucleotide (25-mer) HG U133A 2.0 microarray platform were compared, and the correlation coefficient (R value) between the two platforms was 0.787 when the total of 6754 common genes were detected using the two platforms, employing the same batch of RNA extracted from HeLa and HEK293 cell lines. (B) Self-to-self comparison of the gene expression. For each test and control sample, two hybridizations were performed by using a reversal fluorescence strategy. The change of magnitude of self-to-self expression profiling was within twofold, which indicated that a change less than twofold could be considered to represent the noise level of the microarray experiment. The two lines parallel in the graph represent 2- and 0.5-fold changes in expression. (C) The determination of global gene expression of HepG2.2.15 versus HepG2 cells was repeated three times independently. For each test and control sample in one independent experiment, two hybridizations were performed by using a reverse fluorescence strategy. Two sets of the expression ratios were chosen to determine the reproducibility of microarray results. The Pearson linear correlation coefficient value (R) was 0.956. (D) Comparison of expression measurement by quantitative RT-PCR and microarray. The expression changes in the selected 17 genes showed good agreement between the two methods.

Article Snippet: The reason for this is that the fidelity of our microarray is twofold; therefore, genes with a change of less than twofold fell into the “gray zone” of microarray analysis, which means that the calculated up- or down-regulation change of these genes may not be precise, and hence it is reasonable to conclude that parts of these five genes may have some disparities in terms of their regulation changes when the two methodologies were applied. fig ft0 fig mode=article f1 fig/graphic|fig/alternatives/graphic mode="anchored" m1 Open in a separate window FIG. 7. caption a7 The fidelity and reproducibility of microarray profiling. (A) The CapitalBio's long oligonucleotide (Operon 70-mer) microarray and Affymetrix's short oligonucleotide (25-mer) HG U133A 2.0 microarray platform were compared, and the correlation coefficient (R value) between the two platforms was 0.787 when the total of 6754 common genes were detected using the two platforms, employing the same batch of RNA extracted from HeLa and HEK293 cell lines. (B) Self-to-self comparison of the gene expression.

Techniques: Microarray, Expressing, Fluorescence, Quantitative RT-PCR