FIRE

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Clustered C. elegans microarray compendium (Kim et al, 2001)

Summary

FIRE has discovered 94 motifs from the query data, consisting of 61 from DNA and 33 from RNA.

Combined DNA and RNA results

Figures
FIRE p-value matrix PDF PNG EPS
FIRE density matrix PDF PNG EPS
FIRE motif interaction matrix PDF PNG EPS
Motif maps
Motif Location    Position   
bias		 Orientation
bias		 Maps
.[CU].[ACU]CCCC.3'UTRYY PDF PNG EPS
.A.[CT]GCGC[CGT]5'Y PDF PNG EPS
[CGT]CTTATC[AT].5'Y PDF PNG EPS
[AGT]CG[ACG]G[AT]C[CG].5' PDF PNG EPS
[ACT][AC]CGTG[AG][AC][AC]5'Y PDF PNG EPS
.AATCGAT.5' PDF PNG EPS
.UUCU[AU]U[CU][CGU]3'UTRY PDF PNG EPS
[ACT][CG]TC[CT]CTC.5' PDF PNG EPS
.[ACG]UC[AU]U[ACU]C[ACU]3'UTRY PDF PNG EPS
.[GU][AC]UC[CU]C[GU].3'UTRY PDF PNG EPS
..GGGGG.[CGT]5' PDF PNG EPS
[CGU][CU][CU]GUU[ACG][CU][CU]3'UTRYY PDF PNG EPS
.CGC[AT][CG]A[CG][AGT]5' PDF PNG EPS
.CGAAGA[ACT][AGT]5' PDF PNG EPS
[CU]C[ACG]U[GU][GU]U[AU][CU]3'UTRY PDF PNG EPS
[CT]TTCGC[AG][AG].5' PDF PNG EPS
.AA[AG]UAAA.3'UTRYY PDF PNG EPS
.CG[AG]GCG..5' PDF PNG EPS
[CGU]UGUA.AU[ACU]3'UTRYY PDF PNG EPS
[CGT]ACCGTA[CG][ACT]5'Y PDF PNG EPS
[CGU]C[AG]U[AGU]UUC[CGU]3'UTRY PDF PNG EPS
.TCGTC[ACG]A.5' PDF PNG EPS
.[ACT]CAC[GT]CG.5' PDF PNG EPS
[AGT]T[AT]GGTC[AG][AGT]5'Y PDF PNG EPS
[CU][AU]UAUC.[ACU][ACU]3'UTRY PDF PNG EPS
[AG][ACG]A[ACG]AG[AGU]U.3'UTRY PDF PNG EPS
.[AG]G[GT][ACT]AGG[CT]5' PDF PNG EPS
.CCG[ACT]CG[ACG][AGT]5' PDF PNG EPS
[AGT][CT]ACAC[AT]C.5' PDF PNG EPS
[GU].UAU[ACU][CG]C[ACU]3'UTRY PDF PNG EPS
[GT][AT]GCG[GT]AC.5' PDF PNG EPS
[AGU]..GGC[AC][AU].3'UTRY PDF PNG EPS
[CG].[CG]CTGG[AG][ACT]5' PDF PNG EPS
.CG[CG]TG[CGT]A[AGT]5' PDF PNG EPS
[AGT]CGA[ACT][ACT]GC.5'Y PDF PNG EPS
.TCC[AT]CG[ACG].5' PDF PNG EPS
[ACU]UCCC[AU]U[AC].3'UTRY PDF PNG EPS
[CU]CUU[AC][ACU]UC[CGU]3'UTRY PDF PNG EPS
.A[AG]UC[CU]C[ACU][ACU]3'UTRY PDF PNG EPS
[ACG]GA[AT][GT]C[GT]C[CGT]5'Y PDF PNG EPS
[AGU]UU[GU][AGU]GAA[ACG]3'UTRY PDF PNG EPS
.ATTCGAA[AGT]5'Y PDF PNG EPS
[CGT]C[CG]T[CT]CTC.5'Y PDF PNG EPS
[AC]CCT[AG][CGT][CT]A.5' PDF PNG EPS
[CU]UC[AGU]C[CG][AGU]U[CU]3'UTRY PDF PNG EPS
[ACU][CU]CGU[GU]U[ACG][ACU]3'UTRY PDF PNG EPS
.TGATA[AG]C[ACG]5'Y PDF PNG EPS
[AGT]AC[AG][AC]CG[AC][AGT]5' PDF PNG EPS
[CGT]C[AGT][CT]CA[ACG]GA5' PDF PNG EPS
[ACU][AGU]CGGGU..3'UTRY PDF PNG EPS
[AGU][GU]C[ACG]CUC[CU][CU]3'UTRY PDF PNG EPS
[ACT][AG]CTACA[AC][ACT]5'Y PDF PNG EPS
[CU]C[ACG][AG]UU[AC]U.3'UTRY PDF PNG EPS
.TACC[AT]AA.5' PDF PNG EPS
[AGU][ACG][AGU]ACAU[AG][CGU]3'UTRY PDF PNG EPS
[GT]A[AT]TTACG[ACG]5'Y PDF PNG EPS
.ATGT[AC]TA.5' PDF PNG EPS
[AGT][AC]GA[AT]AGA[AG]5' PDF PNG EPS
[AGU]AAAAA[CU]U.3'UTRY PDF PNG EPS
.[GT]CTCGA[AT][CGT]5' PDF PNG EPS
.CG.AC[CG]G.5' PDF PNG EPS
.C[GU]C[AGU]UC[AGU][AGU]3'UTRY PDF PNG EPS
[ACU]CCCGA[AU]U[CGU]3'UTRY PDF PNG EPS
.C[CG]G[ACT]ATC[CGT]5'Y PDF PNG EPS
[ACU]U[ACU]A[CU]UA[CU][CU]3'UTRY PDF PNG EPS
[ACG][CG]AC[AG]GC[CG].5' PDF PNG EPS
.[ACG]CTTA[GT]A[ACT]5' PDF PNG EPS
.[CU]AA[ACG]A[CG]A.3'UTRY PDF PNG EPS
.[CT]TTGCGC[ACG]5'Y PDF PNG EPS
.T[CGT]GC[CG]GC[AGT]5' PDF PNG EPS
[ACU]CA[CU]CAU[CG][ACU]3'UTRY PDF PNG EPS
.[CU]UC[AG]C[AU]U[CU]3'UTRY PDF PNG EPS
[CT][AC]T[AG]T[AG][GT]GT5' PDF PNG EPS
.AT[ACT]CGCG.5' PDF PNG EPS
.AACTTTG.5' PDF PNG EPS
[AG]AAAAGAA[ACG]5' PDF PNG EPS
[AG][CG]ACTCCG[ACT]5'Y PDF PNG EPS
.AA[CG][CT]TAG.5'Y PDF PNG EPS
[ACT][CGT]GATCC[ACT][AGT]5' PDF PNG EPS
[CU][CGU][AG]U[CG]UC[AC].3'UTRY PDF PNG EPS
[CG]CTGAAAA[ACT]5' PDF PNG EPS
[ACG]AA[ACG]CGAG.5' PDF PNG EPS
.CAGC[GT]CG[ACT]5' PDF PNG EPS
.UUGUUGA[ACU]3'UTRYY PDF PNG EPS
.UUG[GU]UUC[CGU]3'UTRY PDF PNG EPS
[ACT][AC]CA[AC]CTA.5'Y PDF PNG EPS
[ACT][CT]CAGAC[AT].5'Y PDF PNG EPS
[ACT]CGGC[AGT]C[CG].5'Y PDF PNG EPS
.ACGC[AT][CG]C.5' PDF PNG EPS
[AC][AG]AAA[AG]GG[ACG]5' PDF PNG EPS
.[GT]ACAGTA.5' PDF PNG EPS
[ACT].ACTA[CG]C.5' PDF PNG EPS
[ACT]TTCCAAA[AG]5' PDF PNG EPS
.GA[CGT][AC]GGC.5' PDF PNG EPS
Combined motif maps for co-localizing motifs
Motif 1 Motif 2   Location   Maps
.[CU].[ACU]CCCC..[ACG]UC[AU]U[ACU]C[ACU]3'UTR PDF PNG EPS
.[CU].[ACU]CCCC.[CGU][CU][CU]GUU[ACG][CU][CU]3'UTR PDF PNG EPS
[ACU]U[ACU]A[CU]UA[CU][CU].A[AG]UC[CU]C[ACU][ACU]3'UTR PDF PNG EPS
[CGT]CTTATC[AT]..TGATA[AG]C[ACG]5' PDF PNG EPS
[ACT][AC]CGTG[AG][AC][AC][ACT]TTCCAAA[AG]5' PDF PNG EPS
.A.[CT]GCGC[CGT].TCGTC[ACG]A.5' PDF PNG EPS
[CGT]ACCGTA[CG][ACT][CGT]C[AGT][CT]CA[ACG]GA5' PDF PNG EPS
[CGT]ACCGTA[CG][ACT][ACG]AA[ACG]CGAG.5' PDF PNG EPS
.TCC[AT]CG[ACG].[ACG]GA[AT][GT]C[GT]C[CGT]5' PDF PNG EPS
.C[CG]G[ACT]ATC[CGT].T[CGT]GC[CG]GC[AGT]5' PDF PNG EPS

Additional information for DNA motifs

Best GO enrichments for motifs
All GO enrichments for motifs
All motif occurrences of motifs predicted by FIRE, sorted by putative functionality

Additional information for RNA motifs

Best GO enrichments for motifs
All GO enrichments for motifs
All motif occurrences of motifs predicted by FIRE, sorted by putative functionality

Reference

FIRE is a motif discovery and characterization program based on mutual information.