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MCL coexpression mm9:132: Difference between revisions

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|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0986886653414259,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0245993586654517,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110544086345426,0,0,0,0,0,0.107511441879825,0.0683455646190839,0.100296779313498,0,0,0,0,0,0,0,0,0.122390091620849,0,0,0,0,0,0,0,0,0.0959343498639139,0.310478004014784,0,0,0,0,0.456960520238567,0,0,0.380504223622236,0,0,0,0,0,0,0,0,0,0,0.148404418111199,0.228487367553005,0.0978549673988937,0.0829439327499637,0,0,0,0,0.0285860945550467,0,0,0.055274507402915,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0623063220167371,0,0.058094494212308,0.0407466823303253,0.006986554457587,0.0405352443821034,0.0338533374824575,0.0101240446057175,0.0861996515928926,0.0458966288086988,0,0,0,0.257010548932497,0.0839639919176933,0.229607623464208,0.279227004804929,0.350060394277439,0.443892352230382,0.48016456573643,0.52797066997704,0.435859715607959,0.478664838509681,0.460653416684375,0.543296883391622,0.446791645189773,0.522420651472323,0.458056252045688,0,0,0,0,0,0.0829315915550757,0.0499337563906411,0.00204553996582984,0.0183514945589927,0.0242643863559937,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.191523550257637,0.0753613107413788,0.122520581474887,0.126939531339452,0.091558018055706,0.0672592169170953,0.0927359537809747,0.0774164737207147,0.163729231264335,0.159245076116426,0.159697114913116,0.196283184962967,0.135534238531519,0.156533152932051,0,0,0.173700201812769,0.190856315052995,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.314568789879346,0,0.0655375003561515,0.601272677441165,0,0,0,0,0,0.116420155980149,0.0998284739419172,0,0,0.383277634268158,0,0,0,0,0,0,0,0,0,0,0,0.0312748694966379,0.403142961038014,0,0,0.0254340553719351,0.0489745727197172,0.0660055475634404,0.45439678627335,0,0,0.0160166890247509,0,0,0,0,0,0,0,0.587038450077457,0.0637715600712905,0.281541774984998,0.476775477973703,0.541750197025507,0.635327023857566,0.735847858678915,0.778179605810861,0.766488606955914,0.639632051701945,0.209873913294111,0,0,0,0,0.0430230693868467,0.034952894157037,0.0481920468563092,0.100511416252052,0.0467298322147277,0.0723514498780235,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0178505548981246,0,0,0,1.28886260387099,0.782720451518608,0.504853945281015,0.359116172185315,0.603082919850199,0,0,0,0,0,0,0,0,0,0,0,0,0,0.000337319044386775,0,0.0548846957687196,0.0871588832444397,0.081359932135904,0.120876255993453,0.0978461107777356,0.098117166361508,0.0750453505157095,0.107523539997041,0.0990244263857601,0.0898139621139603,0,0.0905291472420136,0.0766073954291401,0,0.112067779638927,0.128033729919821,0.0922045916859077,0.092873634605593,0.110822898586572,0.0748964051866952,0.113739655973257,0.0820475773660953,0.101427320830301,0.104353329269123,0.0762704008334215,0.0486884105045233,0.0679670118742406,0.148623245464354,0.0741583999726411,0.101589204255551,0,0.102464332364415,0.155257708002722,0.0727683172824711,0,0
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0986886653414259,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0245993586654517,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.110544086345426,0,0,0,0,0,0.107511441879825,0.0683455646190839,0.100296779313498,0,0,0,0,0,0,0,0,0.122390091620849,0,0,0,0,0,0,0,0,0.0959343498639139,0.310478004014784,0,0,0,0,0.456960520238567,0,0,0.380504223622236,0,0,0,0,0,0,0,0,0,0,0.148404418111199,0.228487367553005,0.0978549673988937,0.0829439327499637,0,0,0,0,0.0285860945550467,0,0,0.055274507402915,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0623063220167371,0,0.058094494212308,0.0407466823303253,0.006986554457587,0.0405352443821034,0.0338533374824575,0.0101240446057175,0.0861996515928926,0.0458966288086988,0,0,0,0.257010548932497,0.0839639919176933,0.229607623464208,0.279227004804929,0.350060394277439,0.443892352230382,0.48016456573643,0.52797066997704,0.435859715607959,0.478664838509681,0.460653416684375,0.543296883391622,0.446791645189773,0.522420651472323,0.458056252045688,0,0,0,0,0,0.0829315915550757,0.0499337563906411,0.00204553996582984,0.0183514945589927,0.0242643863559937,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.191523550257637,0.0753613107413788,0.122520581474887,0.126939531339452,0.091558018055706,0.0672592169170953,0.0927359537809747,0.0774164737207147,0.163729231264335,0.159245076116426,0.159697114913116,0.196283184962967,0.135534238531519,0.156533152932051,0,0,0.173700201812769,0.190856315052995,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.314568789879346,0,0.0655375003561515,0.601272677441165,0,0,0,0,0,0.116420155980149,0.0998284739419172,0,0,0.383277634268158,0,0,0,0,0,0,0,0,0,0,0,0.0312748694966379,0.403142961038014,0,0,0.0254340553719351,0.0489745727197172,0.0660055475634404,0.45439678627335,0,0,0.0160166890247509,0,0,0,0,0,0,0,0.587038450077457,0.0637715600712905,0.281541774984998,0.476775477973703,0.541750197025507,0.635327023857566,0.735847858678915,0.778179605810861,0.766488606955914,0.639632051701945,0.209873913294111,0,0,0,0,0.0430230693868467,0.034952894157037,0.0481920468563092,0.100511416252052,0.0467298322147277,0.0723514498780235,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0178505548981246,0,0,0,1.28886260387099,0.782720451518608,0.504853945281015,0.359116172185315,0.603082919850199,0,0,0,0,0,0,0,0,0,0,0,0,0,0.000337319044386775,0,0.0548846957687196,0.0871588832444397,0.081359932135904,0.120876255993453,0.0978461107777356,0.098117166361508,0.0750453505157095,0.107523539997041,0.0990244263857601,0.0898139621139603,0,0.0905291472420136,0.0766073954291401,0,0.112067779638927,0.128033729919821,0.0922045916859077,0.092873634605593,0.110822898586572,0.0748964051866952,0.113739655973257,0.0820475773660953,0.101427320830301,0.104353329269123,0.0762704008334215,0.0486884105045233,0.0679670118742406,0.148623245464354,0.0741583999726411,0.101589204255551,0,0.102464332364415,0.155257708002722,0.0727683172824711,0,0
|gostat_on_MCL_coexpression=GO:0005856;cytoskeleton;2.67976139878378e-06;192176,17880,27428,11468,93689,13007,68519,17904,107589,98932!GO:0007010;cytoskeleton organization and biogenesis;5.24674647182257e-05;27428,11468,13007,107589,17904,98932,12797!GO:0043232;intracellular non-membrane-bound organelle;9.91431239091097e-05;192176,17880,27428,11468,93689,13007,68519,17904,107589,98932!GO:0043228;non-membrane-bound organelle;9.91431239091097e-05;192176,17880,27428,11468,93689,13007,68519,17904,107589,98932!GO:0015629;actin cytoskeleton;9.93156895294497e-05;11468,13007,17904,17880,98932!GO:0044430;cytoskeletal part;0.000786135012020431;27428,11468,17904,17880,68519,98932!GO:0008092;cytoskeletal protein binding;0.000808385380622275;27428,93689,192176,17880,12797!GO:0030029;actin filament-based process;0.000808385380622275;27428,13007,17904,12797!GO:0007517;muscle development;0.000808385380622275;21345,11468,17904,98932!GO:0008307;structural constituent of muscle;0.000808385380622275;11468,17904!GO:0016459;myosin complex;0.000808385380622275;17904,17880,98932!GO:0003779;actin binding;0.00287244351512375;27428,192176,17880,12797!GO:0006996;organelle organization and biogenesis;0.00287244351512375;27428,11468,13007,107589,17904,98932,12797!GO:0005516;calmodulin binding;0.00415217178145964;107589,17880,12797!GO:0030036;actin cytoskeleton organization and biogenesis;0.0112563239343898;27428,13007,12797!GO:0030485;smooth muscle contractile fiber;0.0173293431216786;17880!GO:0005912;adherens junction;0.0277117578107089;27428,225341!GO:0002066;columnar/cuboidal epithelial cell development;0.0277117578107089;27428!GO:0030049;muscle filament sliding;0.0277117578107089;17904!GO:0002065;columnar/cuboidal epithelial cell differentiation;0.0277117578107089;27428!GO:0044446;intracellular organelle part;0.0301361199638258;192176,17880,20475,27428,11468,68519,17904,98932!GO:0044422;organelle part;0.0301361199638258;192176,17880,20475,27428,11468,68519,17904,98932!GO:0016043;cellular component organization and biogenesis;0.030305584673252;27428,11468,192176,13007,107589,17904,98932,12797!GO:0033275;actin-myosin filament sliding;0.0319575890420853;17904!GO:0004687;myosin light chain kinase activity;0.0319575890420853;107589!GO:0016461;unconventional myosin complex;0.0319575890420853;17904!GO:0003012;muscle system process;0.0349098570917702;17904,17880!GO:0006936;muscle contraction;0.0349098570917702;17904,17880!GO:0045022;early endosome to late endosome transport;0.0381812511230087;192176!
|gostat_on_MCL_coexpression=GO:0005856;cytoskeleton;2.67976139878378e-06;192176,17880,27428,11468,93689,13007,68519,17904,107589,98932!GO:0007010;cytoskeleton organization and biogenesis;5.24674647182257e-05;27428,11468,13007,107589,17904,98932,12797!GO:0043232;intracellular non-membrane-bound organelle;9.91431239091097e-05;192176,17880,27428,11468,93689,13007,68519,17904,107589,98932!GO:0043228;non-membrane-bound organelle;9.91431239091097e-05;192176,17880,27428,11468,93689,13007,68519,17904,107589,98932!GO:0015629;actin cytoskeleton;9.93156895294497e-05;11468,13007,17904,17880,98932!GO:0044430;cytoskeletal part;0.000786135012020431;27428,11468,17904,17880,68519,98932!GO:0008092;cytoskeletal protein binding;0.000808385380622275;27428,93689,192176,17880,12797!GO:0030029;actin filament-based process;0.000808385380622275;27428,13007,17904,12797!GO:0007517;muscle development;0.000808385380622275;21345,11468,17904,98932!GO:0008307;structural constituent of muscle;0.000808385380622275;11468,17904!GO:0016459;myosin complex;0.000808385380622275;17904,17880,98932!GO:0003779;actin binding;0.00287244351512375;27428,192176,17880,12797!GO:0006996;organelle organization and biogenesis;0.00287244351512375;27428,11468,13007,107589,17904,98932,12797!GO:0005516;calmodulin binding;0.00415217178145964;107589,17880,12797!GO:0030036;actin cytoskeleton organization and biogenesis;0.0112563239343898;27428,13007,12797!GO:0030485;smooth muscle contractile fiber;0.0173293431216786;17880!GO:0005912;adherens junction;0.0277117578107089;27428,225341!GO:0002066;columnar/cuboidal epithelial cell development;0.0277117578107089;27428!GO:0030049;muscle filament sliding;0.0277117578107089;17904!GO:0002065;columnar/cuboidal epithelial cell differentiation;0.0277117578107089;27428!GO:0044446;intracellular organelle part;0.0301361199638258;192176,17880,20475,27428,11468,68519,17904,98932!GO:0044422;organelle part;0.0301361199638258;192176,17880,20475,27428,11468,68519,17904,98932!GO:0016043;cellular component organization and biogenesis;0.030305584673252;27428,11468,192176,13007,107589,17904,98932,12797!GO:0033275;actin-myosin filament sliding;0.0319575890420853;17904!GO:0004687;myosin light chain kinase activity;0.0319575890420853;107589!GO:0016461;unconventional myosin complex;0.0319575890420853;17904!GO:0003012;muscle system process;0.0349098570917702;17904,17880!GO:0006936;muscle contraction;0.0349098570917702;17904,17880!GO:0045022;early endosome to late endosome transport;0.0381812511230087;192176!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005153!2.98e-10!17;UBERON:0005409!6.25e-10!47;UBERON:0002048!2.94e-08!14;UBERON:0000117!2.94e-08!14;UBERON:0000171!2.94e-08!14;UBERON:0000170!2.94e-08!14;UBERON:0005597!2.94e-08!14;UBERON:0000118!2.94e-08!14;UBERON:0005157!7.32e-08!20
}}
}}

Revision as of 16:42, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:127929959..127929970,-p5@Myl6
Mm9::chr11:3429559..3429595,-p@chr11:3429559..3429595
-
Mm9::chr11:3429910..3429928,-p@chr11:3429910..3429928
-
Mm9::chr11:3430231..3430242,+p1@ENSMUST00000128806
Mm9::chr11:3430911..3430930,+p2@ENSMUST00000123459
Mm9::chr11:3430935..3430962,+p1@ENSMUST00000123459
Mm9::chr11:62389120..62389144,+p8@Trpv2
Mm9::chr12:109609195..109609235,+p6@Eml1
Mm9::chr12:53891970..53892007,+p@chr12:53891970..53892007
+
Mm9::chr13:47161761..47161770,+p8@Kdm1b
Mm9::chr15:83349375..83349379,-p@chr15:83349375..83349379
-
Mm9::chr16:14205593..14205622,+p@chr16:14205593..14205622
+
Mm9::chr16:14207739..14207746,+p@chr16:14207739..14207746
+
Mm9::chr16:14207779..14207821,+p@chr16:14207779..14207821
+
Mm9::chr16:14209676..14209712,+p@chr16:14209676..14209712
+
Mm9::chr16:14215838..14215863,+p@chr16:14215838..14215863
+
Mm9::chr16:14215953..14215973,+p@chr16:14215953..14215973
+
Mm9::chr16:14218999..14219020,+p@chr16:14218999..14219020
+
Mm9::chr16:14291448..14291464,-p1@Myh11
Mm9::chr16:24448168..24448239,+p3@Lpp
Mm9::chr16:24608381..24608412,-p@chr16:24608381..24608412
-
Mm9::chr16:31455191..31455203,+p@chr16:31455191..31455203
+
Mm9::chr16:31455206..31455220,+p@chr16:31455206..31455220
+
Mm9::chr16:31455226..31455246,+p@chr16:31455226..31455246
+
Mm9::chr16:34921604..34921680,+p2@Mylk
Mm9::chr16:34921700..34921722,+p6@Mylk
Mm9::chr16:34921924..34921933,+p9@Mylk
Mm9::chr16:34922180..34922189,+p@chr16:34922180..34922189
+
Mm9::chr16:34994933..34994955,+p3@Mylk
Mm9::chr16:34994964..34995030,+p1@Mylk
Mm9::chr16:34995031..34995045,+p4@Mylk
Mm9::chr16:34995089..34995104,+p7@Mylk
Mm9::chr16:35000600..35000626,+p@chr16:35000600..35000626
+
Mm9::chr16:35000658..35000665,+p@chr16:35000658..35000665
+
Mm9::chr16:35000672..35000681,-p@chr16:35000672..35000681
-
Mm9::chr16:35000722..35000742,+p@chr16:35000722..35000742
+
Mm9::chr16:35001003..35001026,+p@chr16:35001003..35001026
+
Mm9::chr16:35001539..35001551,+p@chr16:35001539..35001551
+
Mm9::chr17:36004948..36004959,+p@chr17:36004948..36004959
+
Mm9::chr18:32090959..32091002,+p2@Lims2
Mm9::chr18:61825055..61825070,-p2@ENSMUST00000154522
p2@uc008fcj.1
Mm9::chr19:34322534..34322538,-p@chr19:34322534..34322538
-
Mm9::chr19:34328691..34328750,-p@chr19:34328691..34328750
-
Mm9::chr1:135795729..135795750,-p@chr1:135795729..135795750
-
Mm9::chr1:135795765..135795791,-p@chr1:135795765..135795791
-
Mm9::chr1:135795792..135795827,-p@chr1:135795792..135795827
-
Mm9::chr1:136700000..136700011,-p1@uc007cso.2
Mm9::chr1:136700292..136700303,-p4@Ppp1r12b
Mm9::chr1:136700319..136700330,-p5@Ppp1r12b
Mm9::chr1:136700357..136700440,-p1@Ppp1r12b
Mm9::chr1:137221347..137221397,+p1@Lmod1
Mm9::chr1:137221399..137221433,+p2@Lmod1
Mm9::chr1:137625790..137625811,+p1@Csrp1
Mm9::chr1:172040446..172040463,-p6@Ddr2
Mm9::chr1:74073497..74073529,-p@chr1:74073497..74073529
-
Mm9::chr1:74073534..74073545,-p@chr1:74073534..74073545
-
Mm9::chr2:156601179..156601205,+p1@Myl9
Mm9::chr3:102538419..102538453,+p3@Tspan2
Mm9::chr4:122555640..122555671,-p@chr4:122555640..122555671
-
Mm9::chr4:21858830..21858875,+p4@6230409E13Rik
Mm9::chr5:93368946..93368957,+p@chr5:93368946..93368957
+
Mm9::chr6:34696016..34696046,-p@chr6:34696016..34696046
-
Mm9::chr6:34696138..34696159,-p@chr6:34696138..34696159
-
Mm9::chr6:34696219..34696246,-p@chr6:34696219..34696246
-
Mm9::chr6:34696460..34696574,-p@chr6:34696460..34696574
-
Mm9::chr6:83470749..83470762,-p@chr6:83470749..83470762
-
Mm9::chr6:83473160..83473180,+p@chr6:83473160..83473180
+
Mm9::chr6:83473185..83473234,+p@chr6:83473185..83473234
+
Mm9::chr6:83473213..83473234,-p@chr6:83473213..83473234
-
Mm9::chr6:83476873..83476892,-p3@Actg2
Mm9::chr6:83476909..83476927,-p6@Actg2
Mm9::chr6:83477339..83477352,-p5@Actg2
Mm9::chr6:83477360..83477367,-p11@Actg2
Mm9::chr6:83486209..83486224,-p1@Actg2
Mm9::chr6:83486393..83486428,-p7@Actg2
Mm9::chr7:19680063..19680088,+p@chr7:19680063..19680088
+
Mm9::chr8:46849311..46849324,+p30@Sorbs2
Mm9::chr9:21903715..21903731,+p1@Cnn1
Mm9::chr9:21904695..21904709,+p@chr9:21904695..21904709
+
Mm9::chr9:21904713..21904728,+p@chr9:21904713..21904728
+
Mm9::chr9:21905519..21905577,+p@chr9:21905519..21905577
+
Mm9::chr9:21905634..21905650,+p@chr9:21905634..21905650
+
Mm9::chr9:21905651..21905666,+p@chr9:21905651..21905666
+
Mm9::chr9:21912544..21912557,+p@chr9:21912544..21912557
+
Mm9::chr9:45738439..45738450,+p@chr9:45738439..45738450
+
Mm9::chr9:45743970..45743986,-p1@Tagln
Mm9::chr9:66895960..66895975,-p@chr9:66895960..66895975
-
Mm9::chrX:71495158..71495179,-p2@Flna


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0005856cytoskeleton2.67976139878378e-06
GO:0007010cytoskeleton organization and biogenesis5.24674647182257e-05
GO:0043232intracellular non-membrane-bound organelle9.91431239091097e-05
GO:0043228non-membrane-bound organelle9.91431239091097e-05
GO:0015629actin cytoskeleton9.93156895294497e-05
GO:0044430cytoskeletal part0.000786135012020431
GO:0008092cytoskeletal protein binding0.000808385380622275
GO:0030029actin filament-based process0.000808385380622275
GO:0007517muscle development0.000808385380622275
GO:0008307structural constituent of muscle0.000808385380622275
GO:0016459myosin complex0.000808385380622275
GO:0003779actin binding0.00287244351512375
GO:0006996organelle organization and biogenesis0.00287244351512375
GO:0005516calmodulin binding0.00415217178145964
GO:0030036actin cytoskeleton organization and biogenesis0.0112563239343898
GO:0030485smooth muscle contractile fiber0.0173293431216786
GO:0005912adherens junction0.0277117578107089
GO:0002066columnar/cuboidal epithelial cell development0.0277117578107089
GO:0030049muscle filament sliding0.0277117578107089
GO:0002065columnar/cuboidal epithelial cell differentiation0.0277117578107089
GO:0044446intracellular organelle part0.0301361199638258
GO:0044422organelle part0.0301361199638258
GO:0016043cellular component organization and biogenesis0.030305584673252
GO:0033275actin-myosin filament sliding0.0319575890420853
GO:0004687myosin light chain kinase activity0.0319575890420853
GO:0016461unconventional myosin complex0.0319575890420853
GO:0003012muscle system process0.0349098570917702
GO:0006936muscle contraction0.0349098570917702
GO:0045022early endosome to late endosome transport0.0381812511230087



Relative expression of the co-expression cluster over median <br>Analyst:




Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
epithelial bud2.98e-1017
gastrointestinal system6.25e-1047
lung2.94e-0814
respiratory tube2.94e-0814
respiration organ2.94e-0814
pair of lungs2.94e-0814
lung primordium2.94e-0814
lung bud2.94e-0814
epithelial fold7.32e-0820


TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data

Novel motifs




JASPAR motifs


Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}

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