******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.0 (Release date: 2004/08/18 09:07:01) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.sdsc.edu. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** DATAFILE= downstream.fa4.nr65 ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ miR-124:Mtpn 1.0000 2599 miR-141:CLOCK 1.0000 2592 miR-24:MAPK14 1.0000 1544 miR-145:PARP8 1.0000 120 miR-23a:FLJ13158 1.0000 1330 let-7e:SMCL1 1.0000 5766 miR-199b:LAMC2 1.0000 1183 miR-23:HES1:2 1.0000 163 miR-20a:E2F1:1 1.0000 550 miR-196:HOXB8 1.0000 326 miR143:ERK5:1 1.0000 81 miR-1:Hand2 1.0000 1977 miR-1:TB4 1.0000 280 miR-23:POU4F2:1 1.0000 1455 miR-101:Enx-1:1 1.0000 98 miR-101:MYCN:1 1.0000 309 miR-19a:PTEN:1 1.0000 656 miR-34:DLL1:1 1.0000 359 miR-1b:G6PD:1 1.0000 408 miR-1b:BDNF:1 1.0000 2599 miR-26:SMAD1:1 1.0000 1084 let-7:KRAS:1 1.0000 4275 let-7:NRAS:1 1.0000 836 miR-15:BCL2 1.0000 2645 miR-132:RICS/p250GAP:1 1.0000 812 miR-223:NFIA:1 1.0000 127 miR-133:SRF:1 1.0000 1899 miR-10a:HOXA1:1 1.0000 760 miR-155:AGTR1(1) 1.0000 697 miR-127:BCL6(1) 1.0000 391 miR-140:HDAC4(1) 1.0000 3852 miR-17-5p:AIB1(1) 1.0000 2049 miR-27b:CYP1B1(1) 1.0000 271 miR-206:Fstl1(1) 1.0000 454 miR-189:SLITRK1(1) 1.0000 1413 miR-206:GJA1(1) 1.0000 1146 miR-29:Tcl1(1) 1.0000 372 miR-122:CAT-1(1) 1.0000 3868 miR-125a:ERBB2(1) 1.0000 475 miR-125a:ERBB3(1) 1.0000 1164 miR-133:PTBP2(1) 1.0000 1205 miR-34a:E2F3(1) 1.0000 445 miR-192:SIP1(1) 1.0000 372 let-7a:NF2(1) 1.0000 1561 miR-376a-5p:SFRS11(1) 1.0000 312 miR-376a-5p:SLC16A1(1) 1.0000 1483 miR-376a-5p:TTK(1) 1.0000 138 Edited-miR-376a-5p:PRPS1 1.0000 855 Edited-miR-376a-5p:ZNF51 1.0000 74 Edited-miR-376a-5p:SNX19 1.0000 2072 miR-208:THRAP1(1) 1.0000 117 miR-29b:MCL1(1) 1.0000 1383 miR-1:KCNJ2(1) 1.0000 2535 HSV1-miR-LAT:TGFB1(1) 1.0000 166 HSV1-miR-LAT:SMAD3(1) 1.0000 4042 miR-98:HMGA2(1) 1.0000 2869 miR-206:ESR1(1) 1.0000 4091 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme model: mod= zoops nmotifs= 1 evt= inf object function= E-value of product of p-values width: minw= 8 maxw= 50 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 57 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 76705 N= 57 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.286 C 0.194 G 0.206 T 0.314 Background letter frequencies (from dataset with add-one prior applied): A 0.286 C 0.194 G 0.206 T 0.314 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 50 sites = 12 llr = 430 E-value = 1.0e-046 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 221:323:333:11::45::::8::1511:63263:21:613:5349:35 pos.-specific C 1::4:71634:681332:387a::9627381:1::18::::17223:114 probability G 85:571534:3111711511::2a11111:378:89::a4971143195: matrix T :391:112:343:8:63:613::::33252:1:4:::9::::332:::11 bits 2.4 * * * 2.1 * * * 1.9 * ** * * * * 1.7 * ** * ** * * * Information 1.4 * * * * ** * *** * * ** content 1.2 * * * * * ****** * * ***** * ** (51.7 bits) 0.9 * *** * ** * * ****** * ** ********* ** 0.7 * **** ** ** ** ******** * ************** ** * 0.5 ********** ***** ********* * ************** ***** 0.2 **************** ********************************* 0.0 -------------------------------------------------- Multilevel GGTGGCGCGCTCCTGTAATCCCAGCCACTCAGGAGGCTGAGGCAGAAGGA consensus T CA AGCAGT CCTGC T TT C GA TA G ATTAC AC sequence ATA G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------------------------------------- miR-17-5p:AIB1(1) 1038 3.79e-25 AGCCGGGCAC GGTGGCAGGCACCTGTAATCCCAGCCACTCAGGAGGCTGAGGCACAAGAA TCGCTTGAAC miR-122:CAT-1(1) 1965 8.57e-24 AGCTGGGCAC GTTGGCGCATGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGCC TCAGATCCAA Edited-miR-376a-5p:SNX19 1015 2.75e-23 AGCTGGGTGT GGTGGTGCGCACCTGTAATCCCAGCCACTCAGAAGGCTGAGGCAGGAGAA TTGCTTGAAC miR-20a:E2F1:1 28 3.76e-22 AGCCAGGCAT GATGGGGCGCACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCATAAGAA TCACTTGAAC HSV1-miR-LAT:SMAD3(1) 360 2.36e-20 AGCCAGGTGT GGTGGCATGTGCCTGTGGTCCCAGCTGCTCAGGAGGCTGAGGTGGAAGGA TTGCTTAAGC miR-125a:ERBB3(1) 517 4.21e-19 AGTCGGGCAT GGTGGCTCATGCCTGTAATCTCAGCACTTTGGGAGGCTGAGGCAGAAGGA TTACCTGAGG miR-1b:BDNF:1 2418 8.01e-19 CGCTTCCCGG GTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGC GCCCGCCACC let-7a:NF2(1) 629 2.84e-16 CGCCTCCCGG ATTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGC ACGCACCTCC let-7:KRAS:1 2084 1.75e-15 CATCTCCCAG GTTCAAGCGATTCTCGTGCCTCGGCCTCCTGAGTAGCTGGGATTACAGGC GTGTGCCACT miR-133:SRF:1 716 6.60e-13 CACGCATGGG CATTGCAGCCTTGCGCTGTCCCAGGCATGCAGCTGCCTGGGGCCCAAGTT GCAGTGAGCA miR-29:Tcl1(1) 92 3.39e-12 CCACATCCCG GGACGCAGCAGGAGGCCAGGCCGGCGAGCCCTGTGGATGAGCCCTCAGAA CCCTTGGCTT miR-1b:G6PD:1 32 6.01e-12 CCAGGAGCTG AGTCACCTCCTCCACTCACTCCAGCCCAACAGAAGGAAGGAGGAGGGCGC CCATTCGTCT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- miR-17-5p:AIB1(1) 3.8e-25 1037_[1]_962 miR-122:CAT-1(1) 8.6e-24 1964_[1]_1854 Edited-miR-376a-5p:SNX19 2.8e-23 1014_[1]_1008 miR-20a:E2F1:1 3.8e-22 27_[1]_473 HSV1-miR-LAT:SMAD3(1) 2.4e-20 359_[1]_3633 miR-125a:ERBB3(1) 4.2e-19 516_[1]_598 miR-1b:BDNF:1 8e-19 2417_[1]_132 let-7a:NF2(1) 2.8e-16 628_[1]_883 let-7:KRAS:1 1.7e-15 2083_[1]_2142 miR-133:SRF:1 6.6e-13 715_[1]_1134 miR-29:Tcl1(1) 3.4e-12 91_[1]_231 miR-1b:G6PD:1 6e-12 31_[1]_327 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=50 seqs=12 miR-17-5p:AIB1(1) ( 1038) GGTGGCAGGCACCTGTAATCCCAGCCACTCAGGAGGCTGAGGCACAAGAA 1 miR-122:CAT-1(1) ( 1965) GTTGGCGCATGCCTGTAGTCCCAGCTACTCAGGAGGCTGAGGCAGGAGCC 1 Edited-miR-376a-5p:SNX19 ( 1015) GGTGGTGCGCACCTGTAATCCCAGCCACTCAGAAGGCTGAGGCAGGAGAA 1 miR-20a:E2F1:1 ( 28) GATGGGGCGCACCTGTAATCCCAGCTACTCAGGAGGCTGAGGCATAAGAA 1 HSV1-miR-LAT:SMAD3(1) ( 360) GGTGGCATGTGCCTGTGGTCCCAGCTGCTCAGGAGGCTGAGGTGGAAGGA 1 miR-125a:ERBB3(1) ( 517) GGTGGCTCATGCCTGTAATCTCAGCACTTTGGGAGGCTGAGGCAGAAGGA 1 miR-1b:BDNF:1 ( 2418) GTTCACGCCATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGACTACAGGC 1 let-7a:NF2(1) ( 629) ATTCAAGCAATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGC 1 let-7:KRAS:1 ( 2084) GTTCAAGCGATTCTCGTGCCTCGGCCTCCTGAGTAGCTGGGATTACAGGC 1 miR-133:SRF:1 ( 716) CATTGCAGCCTTGCGCTGTCCCAGGCATGCAGCTGCCTGGGGCCCAAGTT 1 miR-29:Tcl1(1) ( 92) GGACGCAGCAGGAGGCCAGGCCGGCGAGCCCTGTGGATGAGCCCTCAGAA 1 miR-1b:G6PD:1 ( 32) AGTCACCTCCTCCACTCACTCCAGCCCAACAGAAGGAAGGAGGAGGGCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 73912 bayes= 13.0358 E= 1.0e-046 -78 -122 186 -1023 -78 -1023 128 8 -177 -1023 -1023 154 -1023 110 128 -191 22 -1023 169 -1023 -78 178 -130 -191 22 -122 128 -191 -1023 159 28 -91 -19 78 102 -1023 22 110 -1023 -33 -19 -1023 69 41 -1023 159 -130 8 -177 210 -130 -1023 -177 -122 -130 125 -1023 78 169 -1023 -1023 78 -130 89 54 -22 -130 8 81 -1023 128 -1023 -1023 78 -130 89 -1023 210 -130 -191 -1023 178 -1023 8 -1023 237 -1023 -1023 154 -1023 -31 -1023 -1023 -1023 228 -1023 -1023 224 -130 -1023 -177 159 -130 -33 81 -22 -130 -33 -177 178 -130 -91 -177 78 -130 67 -1023 210 -1023 -91 103 -122 69 -1023 -19 -1023 169 -191 -78 -122 186 -1023 103 -1023 -1023 41 -19 -1023 186 -1023 -1023 -122 215 -1023 -78 210 -1023 -1023 -177 -1023 -1023 154 -1023 -1023 228 -1023 103 -1023 102 -1023 -177 -1023 215 -1023 -19 -122 169 -1023 -1023 178 -130 -33 81 -22 -130 -33 -19 -22 102 -91 54 78 28 -1023 168 -1023 -130 -1023 -1023 -122 215 -1023 22 -122 128 -191 81 110 -1023 -191 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 12 E= 10.0e-047 0.166667 0.083333 0.750000 0.000000 0.166667 0.000000 0.500000 0.333333 0.083333 0.000000 0.000000 0.916667 0.000000 0.416667 0.500000 0.083333 0.333333 0.000000 0.666667 0.000000 0.166667 0.666667 0.083333 0.083333 0.333333 0.083333 0.500000 0.083333 0.000000 0.583333 0.250000 0.166667 0.250000 0.333333 0.416667 0.000000 0.333333 0.416667 0.000000 0.250000 0.250000 0.000000 0.333333 0.416667 0.000000 0.583333 0.083333 0.333333 0.083333 0.833333 0.083333 0.000000 0.083333 0.083333 0.083333 0.750000 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.083333 0.583333 0.416667 0.166667 0.083333 0.333333 0.500000 0.000000 0.500000 0.000000 0.000000 0.333333 0.083333 0.583333 0.000000 0.833333 0.083333 0.083333 0.000000 0.666667 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.916667 0.083333 0.000000 0.083333 0.583333 0.083333 0.250000 0.500000 0.166667 0.083333 0.250000 0.083333 0.666667 0.083333 0.166667 0.083333 0.333333 0.083333 0.500000 0.000000 0.833333 0.000000 0.166667 0.583333 0.083333 0.333333 0.000000 0.250000 0.000000 0.666667 0.083333 0.166667 0.083333 0.750000 0.000000 0.583333 0.000000 0.000000 0.416667 0.250000 0.000000 0.750000 0.000000 0.000000 0.083333 0.916667 0.000000 0.166667 0.833333 0.000000 0.000000 0.083333 0.000000 0.000000 0.916667 0.000000 0.000000 1.000000 0.000000 0.583333 0.000000 0.416667 0.000000 0.083333 0.000000 0.916667 0.000000 0.250000 0.083333 0.666667 0.000000 0.000000 0.666667 0.083333 0.250000 0.500000 0.166667 0.083333 0.250000 0.250000 0.166667 0.416667 0.166667 0.416667 0.333333 0.250000 0.000000 0.916667 0.000000 0.083333 0.000000 0.000000 0.083333 0.916667 0.000000 0.333333 0.083333 0.500000 0.083333 0.500000 0.416667 0.000000 0.083333 -------------------------------------------------------------------------------- Time 659.24 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- miR-124:Mtpn 6.57e-01 2599 miR-141:CLOCK 9.72e-01 2592 miR-24:MAPK14 1.48e-01 1544 miR-145:PARP8 2.70e-01 120 miR-23a:FLJ13158 1.46e-01 1330 let-7e:SMCL1 4.14e-02 985_[1(2.97e-05)]_2302_[1(7.98e-05)]_1967_[1(7.40e-06)]_155_[1(6.68e-05)]_157 miR-199b:LAMC2 7.96e-01 1183 miR-23:HES1:2 4.79e-01 163 miR-20a:E2F1:1 1.88e-19 27_[1(3.76e-22)]_392_[1(3.05e-09)]_31 miR-196:HOXB8 5.01e-01 326 miR143:ERK5:1 4.60e-01 81 miR-1:Hand2 1.52e-01 1117_[1(8.56e-05)]_810 miR-1:TB4 9.80e-02 280 miR-23:POU4F2:1 8.65e-01 1455 miR-101:Enx-1:1 6.48e-01 98 miR-101:MYCN:1 9.89e-01 309 miR-19a:PTEN:1 2.07e-01 656 miR-34:DLL1:1 9.28e-01 359 miR-1b:G6PD:1 2.16e-09 31_[1(6.01e-12)]_22_[1(2.31e-05)]_156_[1(9.68e-05)]_49 miR-1b:BDNF:1 2.04e-15 2417_[1(8.01e-19)]_132 miR-26:SMAD1:1 8.48e-01 1084 let-7:KRAS:1 7.39e-12 2083_[1(1.75e-15)]_2142 let-7:NRAS:1 8.57e-01 836 miR-15:BCL2 3.83e-02 1316_[1(1.50e-05)]_1279 miR-132:RICS/p250GAP:1 4.34e-01 812 miR-223:NFIA:1 5.29e-03 2_[1(6.80e-05)]_75 miR-133:SRF:1 1.22e-09 492_[1(5.18e-05)]_100_[1(1.53e-05)]_23_[1(6.60e-13)]_616_[1(4.01e-05)]_468 miR-10a:HOXA1:1 4.16e-01 760 miR-155:AGTR1(1) 7.50e-01 697 miR-127:BCL6(1) 5.95e-01 391 miR-140:HDAC4(1) 2.70e-01 440_[1(8.27e-05)]_3362 miR-17-5p:AIB1(1) 7.57e-22 902_[1(2.00e-10)]_85_[1(3.79e-25)]_962 miR-27b:CYP1B1(1) 8.82e-01 271 miR-206:Fstl1(1) 1.26e-01 454 miR-189:SLITRK1(1) 7.54e-01 1413 miR-206:GJA1(1) 5.27e-01 1146 miR-29:Tcl1(1) 1.10e-09 91_[1(3.39e-12)]_231 miR-122:CAT-1(1) 3.27e-20 47_[1(4.95e-17)]_1867_[1(8.57e-24)]_1854 miR-125a:ERBB2(1) 1.49e-02 242_[1(3.51e-05)]_183 miR-125a:ERBB3(1) 4.70e-16 223_[1(3.20e-05)]_243_[1(4.21e-19)]_108_[1(6.85e-07)]_440 miR-133:PTBP2(1) 6.05e-01 1205 miR-34a:E2F3(1) 8.81e-02 445 miR-192:SIP1(1) 3.26e-01 372 let-7a:NF2(1) 4.30e-13 13_[1(1.47e-07)]_357_[1(4.64e-05)]_158_[1(2.84e-16)]_84_[1(2.26e-08)]_749 miR-376a-5p:SFRS11(1) 9.99e-01 312 miR-376a-5p:SLC16A1(1) 9.84e-01 1483 miR-376a-5p:TTK(1) 5.88e-01 138 Edited-miR-376a-5p:PRPS1 1.36e-02 307_[1(1.69e-05)]_19_[1(9.85e-05)]_429 Edited-miR-376a-5p:ZNF51 1.39e-01 74 Edited-miR-376a-5p:SNX19 5.57e-20 736_[1(1.20e-10)]_93_[1(2.90e-11)]_85_[1(2.75e-23)]_1008 miR-208:THRAP1(1) 6.28e-01 117 miR-29b:MCL1(1) 5.60e-01 1383 miR-1:KCNJ2(1) 2.24e-01 2535 HSV1-miR-LAT:TGFB1(1) 3.90e-01 166 HSV1-miR-LAT:SMAD3(1) 9.41e-17 359_[1(2.36e-20)]_1242_[1(9.10e-07)]_277_[1(9.51e-05)]_2014 miR-98:HMGA2(1) 3.57e-01 2869 miR-206:ESR1(1) 8.86e-01 4091 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 1 reached. ******************************************************************************** CPU: scorpion.binfo.wzw.tum.de ********************************************************************************