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MCL coexpression mm9:478: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000344!2.99e-33!15;UBERON:0000160!2.44e-23!31;UBERON:0001242!4.12e-23!13;UBERON:0000060!4.12e-23!13;UBERON:0001262!4.12e-23!13;UBERON:0004786!4.12e-23!13;UBERON:0004923!1.75e-20!24;UBERON:0000331!1.72e-19!3;UBERON:0002116!1.72e-19!3;UBERON:0001204!1.72e-19!3;UBERON:0001168!1.72e-19!3;UBERON:0005409!5.27e-15!47;UBERON:0002108!8.80e-15!4;UBERON:0001962!3.90e-14!2;UBERON:0001961!3.90e-14!2;UBERON:0001744!3.90e-14!2;UBERON:0003350!2.00e-11!9;UBERON:0004808!2.00e-11!9;UBERON:0001277!2.00e-11!9;UBERON:0002465!9.97e-10!3;UBERON:0000485!2.16e-09!11;UBERON:0003199!6.29e-08!1;UBERON:0001007!7.76e-08!116;UBERON:0001555!7.76e-08!116;UBERON:0007026!7.76e-08!116;UBERON:0004119!1.12e-07!118;UBERON:0000925!1.12e-07!118;UBERON:0006595!1.12e-07!118
|ontology_enrichment_uberon=UBERON:0000344!2.99e-33!15;UBERON:0000160!2.44e-23!31;UBERON:0001242!4.12e-23!13;UBERON:0000060!4.12e-23!13;UBERON:0001262!4.12e-23!13;UBERON:0004786!4.12e-23!13;UBERON:0004923!1.75e-20!24;UBERON:0000331!1.72e-19!3;UBERON:0002116!1.72e-19!3;UBERON:0001204!1.72e-19!3;UBERON:0001168!1.72e-19!3;UBERON:0005409!5.27e-15!47;UBERON:0002108!8.80e-15!4;UBERON:0001962!3.90e-14!2;UBERON:0001961!3.90e-14!2;UBERON:0001744!3.90e-14!2;UBERON:0003350!2.00e-11!9;UBERON:0004808!2.00e-11!9;UBERON:0001277!2.00e-11!9;UBERON:0002465!9.97e-10!3;UBERON:0000485!2.16e-09!11;UBERON:0003199!6.29e-08!1;UBERON:0001007!7.76e-08!116;UBERON:0001555!7.76e-08!116;UBERON:0007026!7.76e-08!116;UBERON:0004119!1.12e-07!118;UBERON:0000925!1.12e-07!118;UBERON:0006595!1.12e-07!118
|tfbs_overrepresentation_for_novel_motifs=0.206403,0.124391,0.186933,0.671595,0.356286,0.250289,0.324772,0.800034,0.0622408,0.0308722,0.288187,0.84479,0.0577792,0.335151,0.769215,0,0.505674,0.34341,0.422292,0.0839024,0.939233,0.010084,0.334384,0.109412,0.192505,0.35869,0.178452,0.267095,0.139679,0.125189,0.255771,0.598971,0.104128,0.15332,0.121176,0.122803,0.0985485,0.311629,0.0859217,0.0703677,0.349739,0.259911,0.438559,0.774932,0.0283033,0.230148,0.433813,0.279902,0.564088,0.141659,0.48979,0.381972,0.281801,0.732469,0.749094,0.341233,0.147717,0.303999,0.166653,0.339495,0.580338,0.390204,0.0681609,0.479581,0.350748,0.516415,0.880067,1.22155,0.576002,1.07689,0.173229,0.218482,0.0113485,0.781142,0.040685,0.335357,0.352807,0.423705,0.564426,0.163487,0.220193,0.521544,1.78663,0.443997,0.671442,0.00202775,0.0546055,0.0305699,1.11664,1.38183,0.947651,0.676142,0.610915,0.738618,0.0836626,0.257625,0.790304,0.613539,0.43404,0.0236008,1.10792,0.59871,0.715894,0.490329,0.489372,0.259558,0.543989,0.276621,0.16693,0.161774,1.10271,0.717588,0.164285,0.292444,0.954503,0.346836,0.0221978,0.241826,0.506861,0.31898,0.786314,0.46068,0.360259,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.115924,0.699779,0.233152,1.97964,0.9301,0.975524,0.477441,0.212784,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,1.11321,1.7082,0.214583,0.111457,0.0314055,0.00817433,0.733963,0.077277,0.352111,0.81211,0.996119,0.128633,1.11626,0.212571,0.93695,1.60892,0.568261,0.199399,0.480505,0.914274,0.323091,0.313326,0.000601576
|tfbs_overrepresentation_for_novel_motifs=0.206403,0.124391,0.186933,0.671595,0.356286,0.250289,0.324772,0.800034,0.0622408,0.0308722,0.288187,0.84479,0.0577792,0.335151,0.769215,0,0.505674,0.34341,0.422292,0.0839024,0.939233,0.010084,0.334384,0.109412,0.192505,0.35869,0.178452,0.267095,0.139679,0.125189,0.255771,0.598971,0.104128,0.15332,0.121176,0.122803,0.0985485,0.311629,0.0859217,0.0703677,0.349739,0.259911,0.438559,0.774932,0.0283033,0.230148,0.433813,0.279902,0.564088,0.141659,0.48979,0.381972,0.281801,0.732469,0.749094,0.341233,0.147717,0.303999,0.166653,0.339495,0.580338,0.390204,0.0681609,0.479581,0.350748,0.516415,0.880067,1.22155,0.576002,1.07689,0.173229,0.218482,0.0113485,0.781142,0.040685,0.335357,0.352807,0.423705,0.564426,0.163487,0.220193,0.521544,1.78663,0.443997,0.671442,0.00202775,0.0546055,0.0305699,1.11664,1.38183,0.947651,0.676142,0.610915,0.738618,0.0836626,0.257625,0.790304,0.613539,0.43404,0.0236008,1.10792,0.59871,0.715894,0.490329,0.489372,0.259558,0.543989,0.276621,0.16693,0.161774,1.10271,0.717588,0.164285,0.292444,0.954503,0.346836,0.0221978,0.241826,0.506861,0.31898,0.786314,0.46068,0.360259,0.422901,1.00724,0.567849,0.331666,0.60459,0.8786,0.115924,0.699779,0.233152,1.97964,0.9301,0.975524,0.477441,0.212784,0.261043,0.927716,1.74768,1.35029,0.884624,0.370659,0.608735,0.483498,0.260275,1.11321,1.7082,0.214583,0.111457,0.0314055,0.00817433,0.733963,0.077277,0.352111,0.81211,0.996119,0.128633,1.11626,0.212571,0.93695,1.60892,0.568261,0.199399,0.480505,0.914274,0.323091,0.313326,0.000601576
|tfbs_overrepresentation_jaspar=MA0003.1;3.17424e-05,MA0004.1;0.67248,MA0006.1;0.118059,MA0007.1;0.227553,MA0009.1;0.623671,MA0014.1;0.0171266,MA0017.1;0.135289,MA0019.1;0.456268,MA0024.1;0.582844,MA0025.1;0.845702,MA0027.1;2.24512,MA0028.1;0.12472,MA0029.1;0.562703,MA0030.1;0.568779,MA0031.1;0.535959,MA0038.1;0.358622,MA0040.1;0.635404,MA0041.1;1.02627,MA0042.1;0.98784,MA0043.1;0.71494,MA0046.1;0.657417,MA0048.1;0.102771,MA0050.1;0.270164,MA0051.1;0.366328,MA0052.1;0.642973,MA0055.1;0.0154075,MA0056.1;0,MA0057.1;0.0204801,MA0058.1;0.501197,MA0059.1;1.00391,MA0060.1;0.071412,MA0061.1;0.615538,MA0063.1;0,MA0066.1;0.349199,MA0067.1;0.953264,MA0068.1;0.235061,MA0069.1;0.643292,MA0070.1;0.634186,MA0071.1;0.269487,MA0072.1;0.626238,MA0073.1;5.71926,MA0074.1;0.318792,MA0076.1;0.148159,MA0077.1;0.605975,MA0078.1;1.02284,MA0081.1;0.56362,MA0083.1;0.714187,MA0084.1;1.27474,MA0087.1;0.673355,MA0088.1;0.143884,MA0089.1;0,MA0090.1;0.212772,MA0091.1;0.696557,MA0092.1;0.213012,MA0093.1;0.809981,MA0095.1;0,MA0098.1;0,MA0100.1;0.309116,MA0101.1;0.182791,MA0103.1;0.439015,MA0105.1;0.147614,MA0106.1;0.401864,MA0107.1;0.428571,MA0108.2;0.476838,MA0109.1;0,MA0111.1;1.85481,MA0113.1;0.377232,MA0114.1;0.291992,MA0115.1;0.717599,MA0116.1;0.117928,MA0117.1;0.686999,MA0119.1;0.183219,MA0122.1;0.705806,MA0124.1;0.901619,MA0125.1;0.830088,MA0130.1;0,MA0131.1;0.452196,MA0132.1;0,MA0133.1;0,MA0135.1;1.77281,MA0136.1;0.335579,MA0139.1;0.20466,MA0140.1;0.30902,MA0141.1;0.155997,MA0142.1;3.29329,MA0143.1;0.391481,MA0144.1;0.0881858,MA0145.1;0.0599431,MA0146.1;0.000953111,MA0147.1;0.31605,MA0148.1;0.252062,MA0149.1;0.18682,MA0062.2;0.0394542,MA0035.2;0.312946,MA0039.2;0.000419395,MA0138.2;0.445088,MA0002.2;0.0572064,MA0137.2;0.467774,MA0104.2;0.229221,MA0047.2;0.357963,MA0112.2;0.0124337,MA0065.2;0.060272,MA0150.1;0.644946,MA0151.1;0,MA0152.1;0.358055,MA0153.1;0.765498,MA0154.1;0.0232776,MA0155.1;0.0729675,MA0156.1;0.147567,MA0157.1;1.23539,MA0158.1;0,MA0159.1;0.101261,MA0160.1;0.254455,MA0161.1;0,MA0162.1;0.0342836,MA0163.1;0.00114117,MA0164.1;0.335886,MA0080.2;0.13897,MA0018.2;0.344133,MA0099.2;0.439458,MA0079.2;1.35155e-07,MA0102.2;1.32652,MA0258.1;0.0789466,MA0259.1;0.0890842,MA0442.1;0
}}
}}

Revision as of 11:49, 23 January 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr10:19399797..19399799,+p@chr10:19399797..19399799
+
Mm9::chr11:8445343..8445345,+p@chr11:8445343..8445345
+
Mm9::chr12:91668902..91668912,+p@chr12:91668902..91668912
+
Mm9::chr13:101017287..101017298,-p1@Naip5
Mm9::chr13:91238101..91238106,+p@chr13:91238101..91238106
+
Mm9::chr18:54586672..54586676,+p@chr18:54586672..54586676
+
Mm9::chr18:82501736..82501745,-p@chr18:82501736..82501745
-
Mm9::chr1:176260649..176260652,+p1@1810030J14Rik
p1@LOC100503310
Mm9::chr1:83832601..83832602,+p@chr1:83832601..83832602
+
Mm9::chr2:81509850..81509853,+p@chr2:81509850..81509853
+
Mm9::chr7:147539463..147539468,+p@chr7:147539463..147539468
+
Mm9::chr7:28886273..28886282,+p13@Fcgbp
Mm9::chr8:22224074..22224079,+p1@Defa25
p1@Gm15299
Mm9::chr8:22583676..22583680,+p1@ENSMUST00000121849
Mm9::chr8:22832496..22832497,+p1@ENSMUST00000121649


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:0007339binding of sperm to zona pellucida0.0363964490813327
GO:0035036sperm-egg recognition0.0363964490813327
GO:0009988cell-cell recognition0.0363964490813327
GO:0007338single fertilization0.0468551383576859
GO:0008037cell recognition0.0468551383576859
GO:0009566fertilization0.0468551383576859



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>

Uber Anatomy
Ontology termp-valuen
mucosa2.99e-3315
intestine2.44e-2331
intestinal mucosa4.12e-2313
anatomical wall4.12e-2313
wall of intestine4.12e-2313
gastrointestinal system mucosa4.12e-2313
organ component layer1.75e-2024
ileal mucosa1.72e-193
ileum1.72e-193
mucosa of small intestine1.72e-193
wall of small intestine1.72e-193
gastrointestinal system5.27e-1547
small intestine8.80e-154
gut-associated lymphoid tissue3.90e-142
mucosa-associated lymphoid tissue3.90e-142
lymphoid tissue3.90e-142
epithelium of mucosa2.00e-119
gastrointestinal system epithelium2.00e-119
intestinal epithelium2.00e-119
lymphoid system9.97e-103
simple columnar epithelium2.16e-0911
egg chamber6.29e-081
digestive system7.76e-08116
digestive tract7.76e-08116
primitive gut7.76e-08116
endoderm-derived structure1.12e-07118
endoderm1.12e-07118
presumptive endoderm1.12e-07118


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)
MA0003.13.17424e-05
MA0004.10.67248
MA0006.10.118059
MA0007.10.227553
MA0009.10.623671
MA0014.10.0171266
MA0017.10.135289
MA0019.10.456268
MA0024.10.582844
MA0025.10.845702
MA0027.12.24512
MA0028.10.12472
MA0029.10.562703
MA0030.10.568779
MA0031.10.535959
MA0038.10.358622
MA0040.10.635404
MA0041.11.02627
MA0042.10.98784
MA0043.10.71494
MA0046.10.657417
MA0048.10.102771
MA0050.10.270164
MA0051.10.366328
MA0052.10.642973
MA0055.10.0154075
MA0056.10
MA0057.10.0204801
MA0058.10.501197
MA0059.11.00391
MA0060.10.071412
MA0061.10.615538
MA0063.10
MA0066.10.349199
MA0067.10.953264
MA0068.10.235061
MA0069.10.643292
MA0070.10.634186
MA0071.10.269487
MA0072.10.626238
MA0073.15.71926
MA0074.10.318792
MA0076.10.148159
MA0077.10.605975
MA0078.11.02284
MA0081.10.56362
MA0083.10.714187
MA0084.11.27474
MA0087.10.673355
MA0088.10.143884
MA0089.10
MA0090.10.212772
MA0091.10.696557
MA0092.10.213012
MA0093.10.809981
MA0095.10
MA0098.10
MA0100.10.309116
MA0101.10.182791
MA0103.10.439015
MA0105.10.147614
MA0106.10.401864
MA0107.10.428571
MA0108.20.476838
MA0109.10
MA0111.11.85481
MA0113.10.377232
MA0114.10.291992
MA0115.10.717599
MA0116.10.117928
MA0117.10.686999
MA0119.10.183219
MA0122.10.705806
MA0124.10.901619
MA0125.10.830088
MA0130.10
MA0131.10.452196
MA0132.10
MA0133.10
MA0135.11.77281
MA0136.10.335579
MA0139.10.20466
MA0140.10.30902
MA0141.10.155997
MA0142.13.29329
MA0143.10.391481
MA0144.10.0881858
MA0145.10.0599431
MA0146.10.000953111
MA0147.10.31605
MA0148.10.252062
MA0149.10.18682
MA0062.20.0394542
MA0035.20.312946
MA0039.20.000419395
MA0138.20.445088
MA0002.20.0572064
MA0137.20.467774
MA0104.20.229221
MA0047.20.357963
MA0112.20.0124337
MA0065.20.060272
MA0150.10.644946
MA0151.10
MA0152.10.358055
MA0153.10.765498
MA0154.10.0232776
MA0155.10.0729675
MA0156.10.147567
MA0157.11.23539
MA0158.10
MA0159.10.101261
MA0160.10.254455
MA0161.10
MA0162.10.0342836
MA0163.10.00114117
MA0164.10.335886
MA0080.20.13897
MA0018.20.344133
MA0099.20.439458
MA0079.21.35155e-07
MA0102.21.32652
MA0258.10.0789466
MA0259.10.0890842
MA0442.10
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