PaGenBase specifications


Unique identifier OMICS_11274
Name PaGenBase
Alternative name Pattern Gene Database
Restrictions to use None
Data access File download, Browse
Version 1.0
Maintained Yes


  • Bacteria
    • Escherichia coli
  • Invertebrates
    • Caenorhabditis elegans
    • Drosophila melanogaster
  • Mammals
    • Bos taurus
  • Plants and Fungi
    • Arabidopsis thaliana
    • Glycine max
    • Saccharomyces cerevisiae
  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
    • Rattus norvegicus
  • Vertebrates
    • Danio rerio


  • person_outline Zhi-Liang Ji

Publication for Pattern Gene Database

PaGenBase citations


Analysis of spatial temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain

Sci Rep
PMCID: 4726224
PMID: 26786896
DOI: 10.1038/srep19274

[…] expressed or unexpressed relative to other substructures over all time points.The quantization procedure is robust against data normalization procedures such as z-scores, rank transform, PaGeFinder, PaGenBase, and TiSGeD since the threshold was obtained from the sorted data point values and the order of data point values is preserved in most normalization procedures. […]


Combining Evidence of Preferential Gene Tissue Relationships from Multiple Sources

PLoS One
PMCID: 3741196
PMID: 23950964
DOI: 10.1371/journal.pone.0070568

[…] e is specifically or ubiquitously expressed across a set of tissues. If a gene is predicted specific, an outlier detection method is used to identify the tissue . Another measure, SPM, is used by the PaGenBase database . It is a normalized specificity measure, based on the expression vector, which is between 0 and 1. A value close to 1 indicates specificity and a value close to 0 indicates ubiquit […]

PaGenBase institution(s)
State Key Laboratory of Stress Cell Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian, China; Department of Chemical Biology, College of Chemistry and Chemical Engineering, The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian, China; School of Information Science and Technology, Xiamen University, Xiamen, Fujian, China

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