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MCL coexpression mm9:224: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000073!5.22e-11!54;UBERON:0002346!7.58e-10!64;UBERON:0003075!7.58e-10!64;UBERON:0007284!7.58e-10!64;UBERON:0001017!1.13e-09!73;UBERON:0001049!2.60e-09!52;UBERON:0005068!2.60e-09!52;UBERON:0006241!2.60e-09!52;UBERON:0007135!2.60e-09!52;UBERON:0001016!3.47e-09!75;UBERON:0002240!9.35e-09!6;UBERON:0005174!9.35e-09!6;UBERON:0001137!9.35e-09!6;UBERON:0002420!1.24e-08!8;UBERON:0007245!1.24e-08!8;UBERON:0010009!1.24e-08!8;UBERON:0010011!1.24e-08!8;UBERON:0000454!1.24e-08!8;UBERON:0004121!2.47e-08!95;UBERON:0000924!2.47e-08!95;UBERON:0006601!2.47e-08!95;UBERON:0001948!3.26e-08!5;UBERON:0002315!3.26e-08!5;UBERON:0003076!4.16e-08!12;UBERON:0003057!4.16e-08!12;UBERON:0010371!1.13e-07!73;UBERON:0002020!2.09e-07!34
|ontology_enrichment_uberon=UBERON:0000073!5.22e-11!54;UBERON:0002346!7.58e-10!64;UBERON:0003075!7.58e-10!64;UBERON:0007284!7.58e-10!64;UBERON:0001017!1.13e-09!73;UBERON:0001049!2.60e-09!52;UBERON:0005068!2.60e-09!52;UBERON:0006241!2.60e-09!52;UBERON:0007135!2.60e-09!52;UBERON:0001016!3.47e-09!75;UBERON:0002240!9.35e-09!6;UBERON:0005174!9.35e-09!6;UBERON:0001137!9.35e-09!6;UBERON:0002420!1.24e-08!8;UBERON:0007245!1.24e-08!8;UBERON:0010009!1.24e-08!8;UBERON:0010011!1.24e-08!8;UBERON:0000454!1.24e-08!8;UBERON:0004121!2.47e-08!95;UBERON:0000924!2.47e-08!95;UBERON:0006601!2.47e-08!95;UBERON:0001948!3.26e-08!5;UBERON:0002315!3.26e-08!5;UBERON:0003076!4.16e-08!12;UBERON:0003057!4.16e-08!12;UBERON:0010371!1.13e-07!73;UBERON:0002020!2.09e-07!34
|tfbs_overrepresentation_for_novel_motifs=0.334203,0.89634,0.533416,0.184237,0.128085,0.199199,2.13566,0.102869,0.222028,0.337168,0.913153,0.289127,2.00733,0.31949,0.054602,0,0.594777,0.96063,0.00960617,0.682411,0.0209942,0.189919,0.318341,0.698529,0.877092,0.355231,0.267563,0.221799,0.185917,0.56829,0.206496,0.276054,0.116565,0.118152,1.09983,0.0499623,0.225878,1.49156,0.535776,0.0188643,0.123465,0.464231,0.34152,0.150649,0.230597,0.173055,0.156727,0.0677314,0.237596,0.0734238,0.194935,0.391414,0.527908,0.384277,0.398303,0.328639,0.647068,0.576361,0.564474,1.11053,1.33354,0.404392,0.057147,0.187777,1.1541,0.613156,0.51212,0.827693,0.258356,0.69152,0.483644,0.0463868,0.215096,0.425631,0.124738,1.44531,0.118032,0.150115,0.249556,0.448606,0.216635,0.621965,0.128113,0.186895,0.333764,0.0142713,1.31408,0.569144,0.159613,0.981395,0.572773,0.337596,0.778619,0.276846,0.0267307,0.674796,0.195348,0.287434,0.474954,0.193095,0.398611,0.275851,0.370402,0.195316,0.567075,0.0581623,0.234223,0.234901,0.745529,0.442482,0.921343,0.371815,0.238327,1.39267,0.578983,0.121437,0.238652,0.419435,1.12617,0.218824,0.430076,0.174742,0.357645,0.456803,0.627117,0.252149,0.648499,0.28043,0.510817,0.0504481,0.35702,1.53572,0.485565,0.106608,0.5981,0.276918,0.038545,0.0588404,0.554766,1.33894,0.950969,0.516174,0.752045,0.774734,0.557152,0.46514,0.479133,1.30006,0.0392346,0.268203,0.086258,0.0915413,1.00201,0.293787,1.15938,0.452379,0.124379,0.0127981,0.0354585,0.151156,1.38342,0.333107,0.703155,0.317802,0.188422,0.335503,0.618764,0.600543,0.09335
|tfbs_overrepresentation_for_novel_motifs=0.334203,0.89634,0.533416,0.184237,0.128085,0.199199,2.13566,0.102869,0.222028,0.337168,0.913153,0.289127,2.00733,0.31949,0.054602,0,0.594777,0.96063,0.00960617,0.682411,0.0209942,0.189919,0.318341,0.698529,0.877092,0.355231,0.267563,0.221799,0.185917,0.56829,0.206496,0.276054,0.116565,0.118152,1.09983,0.0499623,0.225878,1.49156,0.535776,0.0188643,0.123465,0.464231,0.34152,0.150649,0.230597,0.173055,0.156727,0.0677314,0.237596,0.0734238,0.194935,0.391414,0.527908,0.384277,0.398303,0.328639,0.647068,0.576361,0.564474,1.11053,1.33354,0.404392,0.057147,0.187777,1.1541,0.613156,0.51212,0.827693,0.258356,0.69152,0.483644,0.0463868,0.215096,0.425631,0.124738,1.44531,0.118032,0.150115,0.249556,0.448606,0.216635,0.621965,0.128113,0.186895,0.333764,0.0142713,1.31408,0.569144,0.159613,0.981395,0.572773,0.337596,0.778619,0.276846,0.0267307,0.674796,0.195348,0.287434,0.474954,0.193095,0.398611,0.275851,0.370402,0.195316,0.567075,0.0581623,0.234223,0.234901,0.745529,0.442482,0.921343,0.371815,0.238327,1.39267,0.578983,0.121437,0.238652,0.419435,1.12617,0.218824,0.430076,0.174742,0.357645,0.456803,0.627117,0.252149,0.648499,0.28043,0.510817,0.0504481,0.35702,1.53572,0.485565,0.106608,0.5981,0.276918,0.038545,0.0588404,0.554766,1.33894,0.950969,0.516174,0.752045,0.774734,0.557152,0.46514,0.479133,1.30006,0.0392346,0.268203,0.086258,0.0915413,1.00201,0.293787,1.15938,0.452379,0.124379,0.0127981,0.0354585,0.151156,1.38342,0.333107,0.703155,0.317802,0.188422,0.335503,0.618764,0.600543,0.09335
|tfbs_overrepresentation_jaspar=MA0003.1;0.0959022,MA0004.1;1.11818,MA0006.1;0.496256,MA0007.1;0.68365,MA0009.1;0.295418,MA0014.1;0.0879356,MA0017.1;0.876562,MA0019.1;0.171741,MA0024.1;0.728821,MA0025.1;0.48174,MA0027.1;1.83212,MA0028.1;0.529959,MA0029.1;0.248253,MA0030.1;0.252855,MA0031.1;0.64684,MA0038.1;0.719868,MA0040.1;0.30473,MA0041.1;0.115202,MA0042.1;0.104749,MA0043.1;0.369607,MA0046.1;0.32239,MA0048.1;0.113684,MA0050.1;0.489958,MA0051.1;0.367015,MA0052.1;0.310775,MA0055.1;0.428665,MA0056.1;0,MA0057.1;0.734407,MA0058.1;0.748477,MA0059.1;0.109062,MA0060.1;4.80575,MA0061.1;0.0879165,MA0063.1;0,MA0066.1;0.104478,MA0067.1;0.577859,MA0068.1;0.574709,MA0069.1;0.31103,MA0070.1;0.820264,MA0071.1;0.0627582,MA0072.1;0.297449,MA0073.1;0.36079,MA0074.1;0.0876075,MA0076.1;0.203628,MA0077.1;0.769819,MA0078.1;0.817761,MA0081.1;0.303436,MA0083.1;0.965616,MA0084.1;0.878418,MA0087.1;0.335323,MA0088.1;0.0159621,MA0089.1;0,MA0090.1;0.151401,MA0091.1;0.198301,MA0092.1;0.0386321,MA0093.1;1.17817,MA0095.1;0,MA0098.1;0,MA0100.1;0.281053,MA0101.1;0.518315,MA0103.1;0.925959,MA0105.1;0.683736,MA0106.1;0.136153,MA0107.1;0.183235,MA0108.2;0.185867,MA0109.1;0,MA0111.1;0.0427763,MA0113.1;0.76969,MA0114.1;0.539377,MA0115.1;0.371824,MA0116.1;1.4333,MA0117.1;0.346488,MA0119.1;0.280579,MA0122.1;0.362012,MA0124.1;1.31617,MA0125.1;0.468049,MA0130.1;0,MA0131.1;0.168986,MA0132.1;0,MA0133.1;0,MA0135.1;0.398744,MA0136.1;0.0967843,MA0139.1;0.327068,MA0140.1;0.280914,MA0141.1;0.0197122,MA0142.1;0.218511,MA0143.1;0.129679,MA0144.1;0.0296755,MA0145.1;0.236529,MA0146.1;0.0960995,MA0147.1;0.382092,MA0148.1;0.0547891,MA0149.1;0.0292146,MA0062.2;0.119481,MA0035.2;0.28663,MA0039.2;0.090945,MA0138.2;0.954498,MA0002.2;0.198589,MA0137.2;0.019155,MA0104.2;0.23117,MA0047.2;0.109541,MA0112.2;0.0457301,MA0065.2;0.350066,MA0150.1;0.0443275,MA0151.1;0,MA0152.1;0.718358,MA0153.1;0.412245,MA0154.1;0.0234653,MA0155.1;0.994678,MA0156.1;0.0791428,MA0157.1;0.573924,MA0158.1;0,MA0159.1;0.234667,MA0160.1;0.0558568,MA0161.1;0,MA0162.1;0.058162,MA0163.1;0.0739582,MA0164.1;0.0969555,MA0080.2;0.184454,MA0018.2;0.333023,MA0099.2;0.938999,MA0079.2;0.079673,MA0102.2;0.928086,MA0258.1;0.0735493,MA0259.1;0.81249,MA0442.1;0
}}
}}

Revision as of 11:23, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:79957600..79957618,+p1@Onecut3
Mm9::chr10:91627904..91627922,-p1@Rmst
Mm9::chr12:47821823..47821831,-p@chr12:47821823..47821831
-
Mm9::chr12:47919122..47919142,-p@chr12:47919122..47919142
-
Mm9::chr13:95587649..95587666,+p@chr13:95587649..95587666
+
Mm9::chr15:98918857..98918860,-p@chr15:98918857..98918860
-
Mm9::chr16:72027952..72027965,+p@chr16:72027952..72027965
+
Mm9::chr17:37182755..37182764,+p18@Gabbr1
Mm9::chr19:47098299..47098310,+p@chr19:47098299..47098310
+
Mm9::chr19:47098414..47098424,+p@chr19:47098414..47098424
+
Mm9::chr1:122498955..122498968,+p1@En1
Mm9::chr1:122498982..122498991,+p3@En1
Mm9::chr1:122499088..122499099,+p2@En1
Mm9::chr1:140739042..140739054,-p2@Lhx9
Mm9::chr1:19093112..19093124,+p1@Tfap2d
Mm9::chr1:78193687..78193692,-p1@Pax3
Mm9::chr2:181333948..181333966,-p2@Samd10
Mm9::chr2:181333971..181333985,-p3@Samd10
Mm9::chr2:28771056..28771092,-p1@Barhl1
Mm9::chr2:28771380..28771413,-p2@Barhl1
Mm9::chr3:17226363..17226378,-p@chr3:17226363..17226378
-
Mm9::chr4:115612528..115612533,-p1@Dmbx1
Mm9::chr4:130348020..130348047,+p8@Sdc3
Mm9::chr4:53792566..53792578,+p1@Tal2
Mm9::chr5:120881766..120881780,-p@chr5:120881766..120881780
-
Mm9::chr5:120881900..120881914,+p1@Lhx5
Mm9::chr5:120881918..120881921,+p5@Lhx5
Mm9::chr5:120881939..120881946,+p2@Lhx5
Mm9::chr5:137994829..137994836,+p2@Actl6b
Mm9::chr6:138375256..138375268,-p8@Lmo3
Mm9::chr6:138375597..138375621,-p11@Lmo3
Mm9::chr7:116314043..116314071,-p1@Lmo1
Mm9::chr7:17400821..17400830,-p4@Fkrp
Mm9::chr7:56892217..56892221,-p1@Dbx1
Mm9::chr7:58877078..58877091,+p6@Slc17a6
Mm9::chr9:102619607..102619633,+p5@Amotl2
Mm9::chr9:41254760..41254771,+p@chr9:41254760..41254771
+
Mm9::chr9:99776566..99776612,-p1@Sox14
Mm9::chr9:99776617..99776631,-p2@Sox14


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:0003700transcription factor activity4.87239805828158e-07
GO:0043565sequence-specific DNA binding7.50904652949013e-07
GO:0006355regulation of transcription, DNA-dependent1.1901999276898e-06
GO:0044451nucleoplasm part1.1901999276898e-06
GO:0006351transcription, DNA-dependent1.1901999276898e-06
GO:0032774RNA biosynthetic process1.1901999276898e-06
GO:0045449regulation of transcription1.25222133356989e-06
GO:0005654nucleoplasm1.25222133356989e-06
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process1.3522715200986e-06
GO:0006350transcription1.40927872813406e-06
GO:0010468regulation of gene expression1.85839274777677e-06
GO:0031323regulation of cellular metabolic process2.67439720531192e-06
GO:0005667transcription factor complex2.71664147626017e-06
GO:0031981nuclear lumen2.71664147626017e-06
GO:0019222regulation of metabolic process3.21206305699881e-06
GO:0016070RNA metabolic process4.02750325884528e-06
GO:0043233organelle lumen5.3120582662618e-06
GO:0031974membrane-enclosed lumen5.3120582662618e-06
GO:0003677DNA binding5.89520912770347e-06
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process6.87222645177476e-06
GO:0010467gene expression2.23211148596962e-05
GO:0043283biopolymer metabolic process3.39485775885998e-05
GO:0044428nuclear part3.57754438809217e-05
GO:0050789regulation of biological process4.70755603433095e-05
GO:0043234protein complex0.000111908985509395
GO:0050794regulation of cellular process0.000111908985509395
GO:0065007biological regulation0.00012949928815094
GO:0003676nucleic acid binding0.000191543667322009
GO:0043170macromolecule metabolic process0.000592673197893004
GO:0032991macromolecular complex0.000618771760972181
GO:0005634nucleus0.0010018896344164
GO:0007399nervous system development0.00311877579333697
GO:0044238primary metabolic process0.00496102477809034
GO:0044237cellular metabolic process0.00508543312608764
GO:0043231intracellular membrane-bound organelle0.00530114834423677
GO:0043227membrane-bound organelle0.00530114834423677
GO:0007275multicellular organismal development0.00615939336069996
GO:0030902hindbrain development0.0064693499615585
GO:0007420brain development0.0064693499615585
GO:0044446intracellular organelle part0.00914043744565135
GO:0044422organelle part0.00914043744565135
GO:0007417central nervous system development0.0115634810794873
GO:0021915neural tube development0.0138961149319929
GO:0030917midbrain-hindbrain boundary development0.0197354658683251
GO:0004965GABA-B receptor activity0.0197354658683251
GO:0021903rostrocaudal neural tube patterning0.0197354658683251
GO:0043229intracellular organelle0.0215666072893901
GO:0043226organelle0.0215666072893901
GO:0032502developmental process0.028069917852192
GO:0048731system development0.0288922135031901
GO:0005313L-glutamate transmembrane transporter activity0.0335736911544627
GO:0021937Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation0.0335736911544627
GO:0015172acidic amino acid transmembrane transporter activity0.0335736911544627
GO:0016514SWI/SNF complex0.0335736911544627
GO:0001504neurotransmitter uptake0.0384381861901399
GO:0044424intracellular part0.0423670894296677
GO:0021532neural tube patterning0.0423670894296677
GO:0021692cerebellar Purkinje cell layer morphogenesis0.043797599519862
GO:0021940positive regulation of granule cell precursor proliferation0.043797599519862
GO:0021694cerebellar Purkinje cell layer formation0.043797599519862
GO:0021936regulation of granule cell precursor proliferation0.043797599519862
GO:0021702cerebellar Purkinje cell differentiation0.043797599519862
GO:0048513organ development0.0448353612621322
GO:0009954proximal/distal pattern formation0.0448353612621322
GO:0021930granule cell precursor proliferation0.0448353612621322
GO:0021534cell proliferation in hindbrain0.0448353612621322
GO:0021924cell proliferation in the external granule layer0.0448353612621322
GO:0048856anatomical structure development0.0448353612621322
GO:0016564transcription repressor activity0.0454041794967971
GO:0030901midbrain development0.0454041794967971
GO:0021697cerebellar cortex formation0.0454041794967971
GO:0021533cell differentiation in hindbrain0.0454041794967971
GO:0032501multicellular organismal process0.0454041794967971
GO:0008283cell proliferation0.0454041794967971
GO:0016566specific transcriptional repressor activity0.047205899167591
GO:0035115embryonic forelimb morphogenesis0.047205899167591
GO:0005622intracellular0.047205899167591



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>cell_data<br>uberon_data<br><br>


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)
MA0003.10.0959022
MA0004.11.11818
MA0006.10.496256
MA0007.10.68365
MA0009.10.295418
MA0014.10.0879356
MA0017.10.876562
MA0019.10.171741
MA0024.10.728821
MA0025.10.48174
MA0027.11.83212
MA0028.10.529959
MA0029.10.248253
MA0030.10.252855
MA0031.10.64684
MA0038.10.719868
MA0040.10.30473
MA0041.10.115202
MA0042.10.104749
MA0043.10.369607
MA0046.10.32239
MA0048.10.113684
MA0050.10.489958
MA0051.10.367015
MA0052.10.310775
MA0055.10.428665
MA0056.10
MA0057.10.734407
MA0058.10.748477
MA0059.10.109062
MA0060.14.80575
MA0061.10.0879165
MA0063.10
MA0066.10.104478
MA0067.10.577859
MA0068.10.574709
MA0069.10.31103
MA0070.10.820264
MA0071.10.0627582
MA0072.10.297449
MA0073.10.36079
MA0074.10.0876075
MA0076.10.203628
MA0077.10.769819
MA0078.10.817761
MA0081.10.303436
MA0083.10.965616
MA0084.10.878418
MA0087.10.335323
MA0088.10.0159621
MA0089.10
MA0090.10.151401
MA0091.10.198301
MA0092.10.0386321
MA0093.11.17817
MA0095.10
MA0098.10
MA0100.10.281053
MA0101.10.518315
MA0103.10.925959
MA0105.10.683736
MA0106.10.136153
MA0107.10.183235
MA0108.20.185867
MA0109.10
MA0111.10.0427763
MA0113.10.76969
MA0114.10.539377
MA0115.10.371824
MA0116.11.4333
MA0117.10.346488
MA0119.10.280579
MA0122.10.362012
MA0124.11.31617
MA0125.10.468049
MA0130.10
MA0131.10.168986
MA0132.10
MA0133.10
MA0135.10.398744
MA0136.10.0967843
MA0139.10.327068
MA0140.10.280914
MA0141.10.0197122
MA0142.10.218511
MA0143.10.129679
MA0144.10.0296755
MA0145.10.236529
MA0146.10.0960995
MA0147.10.382092
MA0148.10.0547891
MA0149.10.0292146
MA0062.20.119481
MA0035.20.28663
MA0039.20.090945
MA0138.20.954498
MA0002.20.198589
MA0137.20.019155
MA0104.20.23117
MA0047.20.109541
MA0112.20.0457301
MA0065.20.350066
MA0150.10.0443275
MA0151.10
MA0152.10.718358
MA0153.10.412245
MA0154.10.0234653
MA0155.10.994678
MA0156.10.0791428
MA0157.10.573924
MA0158.10
MA0159.10.234667
MA0160.10.0558568
MA0161.10
MA0162.10.058162
MA0163.10.0739582
MA0164.10.0969555
MA0080.20.184454
MA0018.20.333023
MA0099.20.938999
MA0079.20.079673
MA0102.20.928086
MA0258.10.0735493
MA0259.10.81249
MA0442.10
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