CREME pipeline

CREME specifications


Unique identifier OMICS_25389
Alternative name Cis-REgulatory Module Explorer
Interface Web user interface
Restrictions to use None
Input data A set of putatively co-regulated genes.
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes


  • person_outline Ivan Ovcharenko <>
  • person_outline Roded Sharan <>

Publication for Cis-REgulatory Module Explorer

CREME citations

PMCID: 1160116

[…] functional elements; two evolutionary conserved transcription factor analysis tools, rvista and multitf; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ecr browser. here, we briefly describe each one of these tools and provide specific examples […]

PMCID: 1160116

[…] are involved in. creme 2.0 can be used to mine genomic data for initial clues on complex regulatory processes in groups of functionally interconnected genes. we are currently working on expanding creme 2.0 applications to multiple genomes and on providing flexibility in conservation thresholds that could be applied to filtering of tfbs., the rapidly growing collection of sequenced vertebrate […]

CREME institution(s)
International Computer Science Institute, Berkeley, CA, USA; Department of Biochemistry, Stanford University, CA, USA; EEBI and Genome Biology Divisions, L-441 Lawrence Livermore National Laboratory, Livermore, CA, USA
CREME funding source(s)
Supported in part by NSF ITR Grant CCR0121555 and Livermore LDRD Grant 04-ERD-052.

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