Table 2.
Stretch-Regulated Zyxin-Induced Pathways
| No. | Pathway (Source) Functional Description | Stretch vs Quiescent P (NES/FDR) | Stretch vs Quiescent/Zyxin Knockout P (NES/FDR) |
|---|---|---|---|
| 1 | Central nervous system neuron development (GO pathway) | 0.000* (1.95/0.057) | 0.900 (0.68/1.000) |
| 2 | Muscle contraction (GO pathway) | 0.000* (1.94/0.036) | 0.394 (1.02/1.000) |
| 3 | Muscle system process (GO pathway) | 0.000* (1.91/0.045) | 0.406 (1.03/1.000) |
| 4 | Ear morphogenesis (GO pathway) | 0.006* (1.66/0.221) | 0.132 (1.24/1.000) |
| 5 | Forebrain development (GO pathway) | 0.005* (1.64/0.243) | 0.308 (1.07/1.000) |
| 6 | Regionalization (GO pathway) | 0.000* (1.63/0.246) | 0.820 (0.85/1.000) |
| 7 | Inner ear morphogenesis (GO pathway) | 0.008* (1.63/0.242) | 0.114 (1.26/1.000) |
| 8 | Actin cytoskeleton organization and biogenesis (GO pathway) | 0.005* (1.62/0.236) | 0.252 (1.11/1.000) |
| 9 | Blood vessel morphogenesis (GO pathway) | 0.002* (1.62/0.236) | 0.252 (1.09/1.000) |
| 10 | Embryonic morphogenesis (GO pathway) | 0.005* (1.60/0.261) | 0.483 (0.99/1.000) |
| 11 | Ear development (GO pathway) | 0.007* (1.58/0.259) | 0.588 (0.93/1.000) |
| 12 | Cell maturation (GO pathway) | 0.009* (1.57/0.264) | 0.725 (0.86/1.000) |
| 13 | Di-, tri-valent inorganic cation transport (GO pathway) | 0.010* (1.56/0.276) | 0.456 (1.00/1.000) |
| 14 | Actin filament–based process (GO pathway) | 0.003* (1.56/0.275) | 0.244 (1.09/1.000) |
| 15 | Muscle fiber development (GO pathway) | 0.016* (1.55/0.276) | 0.505 (0.97/1.000) |
| 16 | Angiogenesis (GO pathway) | 0.007* (1.54/0.285) | 0.290 (1.07/1.000) |
| 17 | Anatomical structure formation (GO pathway) | 0.005* (1.54/0.283) | 0.424 (1.01/1.000) |
| 18 | Organ morphogenesis (GO pathway) | 0.000* (1.52/0.289) | 0.062 (1.18/1.000) |
| 19 | Vasculature development (GO pathway) | 0.007* (1.51/0.302) | 0.279 (1.07/1.000) |
| 20 | Blood vessel development (GO pathway) | 0.005* (1.51/0.299) | 0.273 (1.07/1.000) |
| 21 | Embryonic development (GO pathway) | 0.000* (1.51/0.290) | 0.332 (1.04/1.000) |
| 22 | Neurogenesis (GO pathway) | 0.002* (1.50/0.285) | 0.599 (0.96/1.000) |
| 23 | Membrane organization and biogenesis (GO pathway) | 0.008* (1.49/0.288) | 0.307 (1.05/1.000) |
| 24 | Cell–cell adhesion (GO pathway) | 0.020* (1.42/0.344) | 0.728 (0.91/1.000) |
| 25 | Cell morphogenesis (GO pathway) | 0.002* (1.42/0.336) | 0.761 (0.92/1.000) |
| 26 | Cellular structure morphogenesis (GO pathway) | 0.001* (1.40/0.355) | 0.715 (0.93/1.000) |
| 27 | Antigen processing and presentation (KEGG) | 0.013* (1.68/0.203) | 0.550 (0.95/1.000) |
| 28 | Dilated cardiomyopathy (KEGG) | 0.004* (1.67/0.187) | 0.721 (0.87/1.000) |
Selective GSEA-pathway analysis of stretch-sensitive genes in mouse aortic VSMCs (third column) and the role of zyxin therein deduced from changes in gene expression following zyxin deficiency (fourth column). Zyxin-induced pathways that respond in similar fashion in both groups are listed. Quiescent state indicates static VSMCs that were unstretched. All pathways are derived from the canonical pathway sets provided by KEGG (http://www.genome.jp/kegg/) and GO (pathways molecular function; http://www.geneontology.org). Only pathways found to be significantly altered (P≤0.02) by cyclic stretch and/or zyxin-deficiency have been included. As an estimate for the actual grade of enrichment and activation/inhibition of a given pathway, NES are listed. Additionally, FDR have been included; a value of FDR ≤0.4 is regarded to be significant. For analyses with altered parameters, please use the raw data provided at NCBI GEO (http://www.ncbi.nlm.nih.gov/geo/query) using the sample number [GSE60447] and the link http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?token=wdorceuihfapraf&acc=GSE60447. In GSEA, the ranking of genes is with respect to the degree of changes in expression. The normalized enrichment score NES reflects the degree to which a pathway (defined by a set of genes) is overrepresented at the top or bottom of this ranked list of genes for a given comparison (eg, quiescent VSMCs vs stretched VSMCs). Thus, a very high value for NES (eg, NES >1.8) reflects a marked activation of the pathway. Accordingly, a value of, eg, NES <−1.6 defines a significant inhibition of the pathway. The false discovery rate FDR enables estimation of the probability that a pathway defined to be significantly regulated by a high NES is falsely positive (eg, FDR=0.4 defines the probability that 6 of 10 predictions by GSEA are correct). The FDR of 1 means 100% (ie, 100% probability of obtaining the observed sample results when the null hypothesis [tested with ANOVA] is actually true). FDR indicates false discovery rates; GO, Gene Ontology; GEO, Gene Expression Omnibus; GSEA, Gene Set Enrichment Analysis; KEGG, Kyoto Encyclopedia of Genes and Genomes; NCBI, National Center for Biotechnology Information; NES, normalized enrichment scores; VSMCs, vascular smooth muscle cells.
P≤0.02.