Journal: Journal of proteome research

Article Title: Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues

doi: 10.1021/acs.jproteome.5b00827

Figure Lengend Snippet: Top 20 Proteins from the 196 Tumor Unique Proteins from the ERBB2+ Gastric Cancer Sample Set

Article Snippet: On the basis of the oncogene list information, for ERBB2+ gastric cancer set, four pathways, namely, ERBB family signaling, development EGFR signaling via small GTPases, development EGFR signaling, and cytoskeleton remodeling integrin outside-in signaling pathway from the GeneGo database, 33 were examined for integration of the proteomic and transcriptomic data and are listed in Supplementary Figure S-4 (a–d).

Techniques: Over Expression, Binding Assay, Expressing, Biomarker Discovery, Marker

Journal: Journal of proteome research

Article Title: Integrated Proteomic and Genomic Analysis of Gastric Cancer Patient Tissues

doi: 10.1021/acs.jproteome.5b00827

Figure Lengend Snippet: ERBB signaling pathway analysis. (a) Summation of the RNA-Seq and proteomic values for genes present in the ERBB signaling pathway from KEGG.34 Red circle: RNA-Seq ≥1 cutoff value. (The red box means the RPKM value is higher than the cut off. The red color is selected only for better clarity. Note this is a different format for visual clarity as the red circles provid best contrast with the green boxes used in the KEGG figures.) Blue cross = RNA-Seq <1. Blue star = proteomics spectral count value >0. Yellow box = proteomics spectral count value >3 only in ERBB2+ tumor sample. (b) Simplified ERBB signaling pathway that lists only the subpathways with a high number of protein observations (ERBB2+ vs ERBB2− patient samples). All genes illustrated have RPKM value >1, green box: spectral counts ≥1; the red star: higher spectral counts in ERBB2+ set (also spectral counts in tumor is higher than control). Note that color is selected only for visual clarity.

Article Snippet: On the basis of the oncogene list information, for ERBB2+ gastric cancer set, four pathways, namely, ERBB family signaling, development EGFR signaling via small GTPases, development EGFR signaling, and cytoskeleton remodeling integrin outside-in signaling pathway from the GeneGo database, 33 were examined for integration of the proteomic and transcriptomic data and are listed in Supplementary Figure S-4 (a–d).

Techniques: RNA Sequencing, Control

Journal: PLoS ONE

Article Title: Cross-Species Genome Wide Expression Analysis during Pluripotent Cell Determination in Mouse and Rat Preimplantation Embryos

doi: 10.1371/journal.pone.0047107

Figure Lengend Snippet: A–B. Scatterplots of the fold changes measured in the three comparisons for 21 members of the FGF factor family ( A. ) and for 7 FGF receptors ( B. ) in the mouse and in the rat. The complete list of all the genes analyzed as well as their fold changes are reported in . C. Fold change scatterplots. Cross species comparison of the fold changes expression of the genes in the pathway “Development, FGFR signaling pathway” from GeneGo (see also ). The data were analyzed as described in . D. Expression signal profile plots. Expression level analysis of 5 selected genes from the FGFR pathway. Mouse: blue; Rat: red; MO: Morula; ICM: Inner cell mass; BL: Blastocyst. The unit is log2 of measured expression.

Article Snippet: The analysis of the pathway “Development FGFR signaling pathway” from GeneGo also highlighted differential expression patterns of genes in the two species ( ).

Techniques: Comparison, Expressing