Shewanella oneidensis cis-Regulatory element database

	Dataset I	Dataset II	Microarray Dataset
The anchor genome (s)	S. oneidensis and E. coli	S. oneidensis	S. oneidensis
Other genomes	At least 1 other Shewanella species	At least 2 other Shewanella species	At least 2 other Shewanella species
Number of promoter sets of orthologous genes	862	1961	460
Step I: Phylogenetic footprinting with iterative CONSENSUS search (Motifs that are conserved across multiple species, redundant)	11247	22525	5355
Step II: PhyloNet Searching (Motifs that are not only conserved across multiple species, but also shared by different genes, still redundant)	203	1665	337
Step III: Motif hierarchical clustering (Final non-redundant motifs)	38* (189**)	183 (824)	31 (124)
Number of motifs matching to known TF binding sites	6	9	4
Number of motifs with GO/KEGG enrichment	6	24	5
Number of motifs with expression coherence	13	46	12
Number of motifs with at least one supporting evidence	16	59	15

^* Number of non-redundant motifs ultimately identified;

^** Number of TUs covered by the predicted motifs..

Click the links to access the detailed information for different datasets.

--- For Bioinformaticians who prefer to parse the results themselves

Download Raw Data (matrix profiles & description files, including the information of site positions in S. oneidensis):

Example of *.desc file

Shewanella_oneidensis_gi24345641_nm1

Matrix:

width = 10

tollr = 72.80

IC = 11.830

P-value = 4.97732E-18

Consensus = AGCcTAgGCT

A | 50 2 2 8 6 47 17 0 0 2

C | 0 6 54 33 2 3 0 2 50 6

G | 6 50 2 0 3 2 33 54 6 0

T | 2 0 0 17 47 6 8 2 2 50

Gene Cluster size = 4:

Shewanella_oneidensis_gi24346409 AGCCTAGGCT -15 12.07 5.915

Shewanella_oneidensis_gi24345641 AGCCTAGGCT -28 12.07 5.915

Shewanella_oneidensis_gi24346539 AGCTTAGGCT -39 11.01 5.915

Shewanella_oneidensis_gi24346298 AGCCAAGGCT -50C (Starting position*) 10.05 (Patser Score) 5.915 (Patser Cutoff)

* The 3'-end promotor starts from -1. "C" means the motif is on the complementary strand.

Summary of Conservation of the known E. coli transcriptional regulatory interactions in S. oneidensis

Shewanella oneidensis cis-Regulatory Element Database