Journal: PLoS ONE

Article Title: Altered Expression of Polycomb Group Genes in Glioblastoma Multiforme

doi: 10.1371/journal.pone.0080970

Figure Lengend Snippet: ( A ) PcG gene expression in TCGA glioblastoma multiforme (GBM) subtypes. Using the TCGA data for GBM, pair-wise comparisons were conducted between all 4 of the molecular subtypes (Mesenchymal, Classical, Neural and Proneural, color coded). ** P<0.01. ( B ) Continuum of abnormal expression in PcG genes in different histological grades of astrocytomas. The Y-axis measures the background adjusted Robust Multi-array Average (RMA) which indicates the normalized expression level. Box-and-whisker plots show the distribution of mRNA expression in normal brain and different grades of astrocytomas (color coded). For detailed statistical analyses, please see & .

Article Snippet: Robust multichip average (RMA) normalization was applied to raw expression TCGA data (.CEL files for Affymetrix arrays) .

Techniques: Expressing, Whisker Assay

Journal: BMC Bioinformatics

Article Title: Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements

doi: 10.1186/1471-2105-6-107

Figure Lengend Snippet: Composition of redefined Affymetrix probe-sets based on overlap with cDNA clone insert sequence. Stacked histograms show the distribution of probe-set size for sets consisting of a single Affymetrix-defined probe-set (black) and for those comprised of probes originally grouped into separate probe-sets by Affymetrix (gray). A , NCI-60 10 k cDNA microarray to HuFL alternative CDF. B , Breast cancer 8 k cDNA microarray to HuFL alternative CDF. C , Breast cancer 8 k cDNA microarray to HG-U95Av2 alternative CDF. D , Lung cancer 22 k cDNA microarray to HG-U95Av2 alternative CDF.

Article Snippet: Raw Affymetrix HG-U95Av2 CEL files were obtained for 199 samples from two additional cohorts of breast cancer patients profiled in previous studies [ , ] and normalized as described above.

Techniques: Sequencing, Microarray

Journal: BMC Bioinformatics

Article Title: Redefinition of Affymetrix probe sets by sequence overlap with cDNA microarray probes reduces cross-platform inconsistencies in cancer-associated gene expression measurements

doi: 10.1186/1471-2105-6-107

Figure Lengend Snippet: Increased efficiency of breast cancer subtype classification transfer from cDNA microarray to Affymetrix HG-U95Av2 gene-chip tumor-profiles by sequence-overlapping probe measurements. Tumor samples profiled on the Affymetrix platform were classified according to their correlation with the set of subtype median-centroids derived from cDNA microarray measurements (see methods). The classified samples were then hierarchically clustered using Pearson correlation and average-linkage agglomeration. ( A ), Affymetrix measurements matched to the cDNA centroids by Unigene identifier. ( B ), Affymetrix measurements matched to cDNA centroids by sequence-overlap of probe features produced more coherent classifications. In particular, the large ERbB2+ subtype cluster (upper left) is mostly absent from the unigene-based classification. The significance of this cluster is supported by the observation that all tumors in this cluster for which Her-2 amplification was assessed by immunohistochemistry were designated positive.

Article Snippet: Raw Affymetrix HG-U95Av2 CEL files were obtained for 199 samples from two additional cohorts of breast cancer patients profiled in previous studies [ , ] and normalized as described above.

Techniques: Microarray, Sequencing, Derivative Assay, Produced, Amplification, Immunohistochemistry

Journal: BMC Genomics

Article Title: Genomic expression during human myelopoiesis

doi: 10.1186/1471-2164-8-264

Figure Lengend Snippet: Gene expression dataset . A) The gene expression dataset analyzed comprises cell samples from different levels of myeloid differentiation process (stem/progenitor cells, precursors and terminally differentiated cells). The graph describes relationships between the cellular contexts analyzed within myeloid differentiation tree. For each cell type, the number of samples examined with independent microarray experiments is indicated in brackets. B) Dendrogram obtained by unsupervised hierarchical clustering on gene expression data matrix. Pearson correlation and average were used as similarity measure and linking method, respectively.

Article Snippet: In particular, raw microarray data (Affymetrix .CEL files) were obtained for a total of 24 samples from 8 different cell types of all myelopoietic lineages, representing a reference dataset for a comprehensive analysis of genomic expression during cell differentiation.

Techniques: Expressing, Microarray