PMC:3475485 / 10880-11934 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3475485","sourcedb":"PMC","sourceid":"3475485","source_url":"https://www.ncbi.nlm.nih.gov/pmc/3475485","text":"Microarray gene expression analysis\nWe used a mouse 30 K whole gene oligonucleotide microarray to identify mRNAs whose expression was altered by the Pkd2 KO and PKD2 TG MEF cells. The normalized log ratios corresponding to each time point were exported to the software for clustering algorithm. We used Axon's Acuity 3.1 (Axon Instruments, Union City, CA, USA) for using the 'gene shaving' algorithm. To estimate the number of clusters in a dataset, we used 'Gap Statistics' in Acuity 3.1. The cluster number estimated by gap statistics was used for an input parameter in gene shaving. After gene shaving, we used a single linkage hierarchical clustering. The single linkage hierarchical clustering method divides 8 'gene shaving' clusters (Fig. 2). The majority of genes whose expression was appreciably altered encoded proteins involved in critical biological processes, such as metabolism, transcription, cell adhesion, cell cycle, and signal transcription. Forty-five genes whose expression was changed by 2-fold or greater were identified (Table 1).","divisions":[{"label":"Title","span":{"begin":0,"end":35}}],"tracks":[]}