microarray comparison analyses  (Keio University Press Inc)

Journal: BMC Cancer

Article Title: Metastatic canine mammary carcinomas can be identified by a gene expression profile that partly overlaps with human breast cancer profiles

doi: 10.1186/1471-2407-10-618

Figure Lengend Snippet: Confirmation of cDNA-Array data by quantitative RT-PCT

Article Snippet: To supplement the gene annotations of the differentially expressed genes with functional information, BLAST search and Affymetrix-provided human to canine microarray comparisons were used to map canine genes to their human equivalents as has been shown before [ ].

Techniques: Microarray

Journal: Arteriosclerosis, Thrombosis, and Vascular Biology

Article Title: Profiling of Atherosclerotic Lesions by Gene and Tissue Microarrays Reveals PCSK6 as a Novel Protease in Unstable Carotid Atherosclerosis

doi: 10.1161/atvbaha.113.301743

Figure Lengend Snippet: Figure 1. Study design. Carotid plaques (n=34) from asymptomatic and symptomatic patients were sectioned at 2 levels and 3 cores drilled from each level (A) to construct 2 tissue microarray (TMA) blocks with 204 cores in total (B). Based on symptomatic vs asymptom- atic microarray comparisons generated for n=127 plaques (C), highly upregulated genes were chosen for the study (D; in red). Several genes already known to be associated with atherosclerosis were also included (D; in black). TMAs were stained by immunohistochemistry (IHC) with antibodies toward human proteins of interest, and tissue sections were scored (0, 1, 2, or 3) for semiquantitative grading of staining intensity (E). Significantly differentially expressed proteins were validated further by IHC on individual plaques (F).

Article Snippet: From the list of highly upregulated genes obtained by microarray comparisons between symptomatic and asymptomatic carotid lesions, candidates with relatively restricted tissue distribution in humans were chosen for further analysis (based on the Human Protein Atlas).

Techniques: Construct, Microarray, Generated, Staining, Immunohistochemistry

Journal: Arteriosclerosis, Thrombosis, and Vascular Biology

Article Title: Profiling of Atherosclerotic Lesions by Gene and Tissue Microarrays Reveals PCSK6 as a Novel Protease in Unstable Carotid Atherosclerosis

doi: 10.1161/atvbaha.113.301743

Figure Lengend Snippet: Figure 4. PCSK6 is the most significantly upregulated proprotein convertase (PC) in symptomatic carotid plaques. Analy- ses of n=127 microarray profiles between carotid plaques (CP) and normal controls (iliac arteries [IA]) show significant down- regulation of Furin and PCSK5 in plaque tissue, upregulation of PCSK6 and PCSK7, whereas PCSK9 and PCSK2 did not exhibit significant variation in expression (A). Posi- tive correlation was found between expres- sion of PCSK6 and PCSK9, PCSK2 and PCSK7, whereas negative was observed with PCSK5 (B). Several PCSK6 isoforms recognized by different Affymetrix probes were significantly upregulated in plaques compared with controls, but most highly the isoform coding for secreted protein (C). This isoform was the only one with signifi- cantly higher expression in comparison between symptomatic (s) and asymptom- atic (as) plaques (D). Results were con- firmed by quantitative real-time polymerase chain reaction (qRT-PCR) analyses for expression of secreted PCSK6 isoform in a separate cohort of n=233 carotid plaques (E and F). Micorarray data expressed as log2 value and qRT-PCR data as fold change compared with control. Data in A, C, and D show mean with SD, whereas median with interquartile range is depicted in E and F. ER indicates endoplasmatic reticulum.

Article Snippet: From the list of highly upregulated genes obtained by microarray comparisons between symptomatic and asymptomatic carotid lesions, candidates with relatively restricted tissue distribution in humans were chosen for further analysis (based on the Human Protein Atlas).

Techniques: Microarray, Expressing, Comparison, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Control