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a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database information

PaGenBase (Pattern Gene Database)

General information

Description: PaGenBase is is a free database that provides information of pattern genes (specific genes, selective genes, housekeeping genes and repressed genes) of 11 model organisms identified from serial gene expression profiles of multiple physiological conditions. PaGenBase has collected 143 quality microarray, NGS and tiling array datasets, as well as the literature, including 1,145,277 profiles. It involves kinds of time/tissue-specific conditions from the aspects of tissue/cell type, development/differention and so on.
Year founded: 2004
Last update: 2013-12-01
Version: v1.0
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Country/Region: China
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Contact information

University/Institution: Xiamen University
Address: Xiamen, Fujian, PR China
City: Xiamen
Province/State: Fujian
Country/Region: China
Contact name (PI/Team): Zhi-Liang Ji
Contact email (PI/Helpdesk):

Record metadata

Created on: 2015-06-30
Curated by:
Shixiang Sun [2016-03-24]
Shixiang Sun [2015-11-19]


All databases:
1377/4549 (69.752%)
254/800 (68.375%)
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PaGenBase: a pattern gene database for the global and dynamic understanding of gene function. [PMID: 24312499]
Pan JB, Hu SC, Shi D, Cai MC, Li YB, Zou Q, Ji ZL.

Pattern genes are a group of genes that have a modularized expression behavior under serial physiological conditions. The identification of pattern genes will provide a path toward a global and dynamic understanding of gene functions and their roles in particular biological processes or events, such as development and pathogenesis. In this study, we present PaGenBase, a novel repository for the collection of tissue- and time-specific pattern genes, including specific genes, selective genes, housekeeping genes and repressed genes. The PaGenBase database is now freely accessible at In the current version (PaGenBase 1.0), the database contains 906,599 pattern genes derived from the literature or from data mining of more than 1,145,277 gene expression profiles in 1,062 distinct samples collected from 11 model organisms. Four statistical parameters were used to quantitatively evaluate the pattern genes. Moreover, three methods (quick search, advanced search and browse) were designed for rapid and customized data retrieval. The potential applications of PaGenBase are also briefly described. In summary, PaGenBase will serve as a resource for the global and dynamic understanding of gene function and will facilitate high-level investigations in a variety of fields, including the study of development, pathogenesis and novel drug discovery.

PLoS One. 2013:8(12) | 31 Citations (from Europe PMC, 2020-02-15)