Modeling and analysis of multi-library, multi-group SAGE data with application to a study of mouse cerebellum.

A serial analysis of gene expression (SAGE) library is a collection of thousands of small DNA "tags," each of which represents a distinct messenger RNA (mRNA) transcript. Existing methods have been proposed for analyzing single library data (i.e.

Serial analysis of gene expression profiles of adult and aged mouse cerebellum.

Changes in specific cerebellar molecules contribute to impaired balance and motor coordination frequently observed in aged individuals. Serial analysis of gene expression (SAGE) was used to construct six libraries from adult and aged mouse cerebella. Combined unique tags for each group revealed 325 genes that were differentially expressed (p-chance View Article and Find Full Text PDF

Human lineage-specific amplification, selection, and neuronal expression of DUF1220 domains.

Extreme gene duplication is a major source of evolutionary novelty. A genome-wide survey of gene copy number variation among human and great ape lineages revealed that the most striking human lineage-specific amplification was due to an unknown gene, MGC8902, which is predicted to encode multiple copies of a protein domain of unknown function (DUF1220). Sequences encoding these domains are virtually all primate-specific, show signs of positive selection, and are increasingly amplified generally as a function of a species' evolutionary proximity to humans, where the greatest number of copies (212) is found.

Digital transcriptome analysis in the aging cerebellum.

Serial analysis of gene expression (SAGE) was used to identify and quantify all expressed cerebellar genes in the adult (P92) and aged (P810) C57BL/6J mouse cerebellum. A "closest-neighbor" algorithm was used to differentiate low abundance tags from possible sequencing errors in both libraries. Unique tags were categorized into four groups: (1) novel genes; (2) ESTs; (3) RIKEN, KIA, and hypothetical genes; and (4) known genes.

Genomic structure and alternative splicing of murine R2B receptor protein tyrosine phosphatases (PTPkappa, mu, rho and PCP-2).

Background: Four genes designated as PTPRK (PTPkappa), PTPRL/U (PCP-2), PTPRM (PTPmu) and PTPRT (PTPrho) code for a subfamily (type R2B) of receptor protein tyrosine phosphatases (RPTPs) uniquely characterized by the presence of an N-terminal MAM domain. These transmembrane molecules have been implicated in homophilic cell adhesion. In the human, the PTPRK gene is located on chromosome 6, PTPRL/U on 1, PTPRM on 18 and PTPRT on 20.