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|ontology_enrichment_disease=DOID:0060100!1.69e-08!3;DOID:4045!1.69e-08!3
|ontology_enrichment_disease=DOID:0060100!1.69e-08!3;DOID:4045!1.69e-08!3
|ontology_enrichment_uberon=UBERON:0002384!3.79e-14!46;UBERON:0002193!5.12e-14!48;UBERON:0002405!5.12e-14!48;UBERON:0002370!5.90e-14!23;UBERON:0000974!5.90e-14!23;UBERON:0004807!5.90e-14!23;UBERON:0005058!5.90e-14!23;UBERON:0003351!5.90e-14!23;UBERON:0009113!5.90e-14!23;UBERON:0003295!5.90e-14!23;UBERON:0009722!5.90e-14!23;UBERON:0005562!5.90e-14!23;UBERON:0007690!5.90e-14!23;UBERON:0002390!1.49e-13!45;UBERON:0003061!1.49e-13!45;UBERON:0006562!2.97e-13!24;UBERON:0003408!2.97e-13!24;UBERON:0001557!2.97e-13!24;UBERON:0001042!2.97e-13!24;UBERON:0008814!2.97e-13!24;UBERON:0009145!2.97e-13!24;UBERON:0004177!3.76e-12!29;UBERON:0005057!3.76e-12!29;UBERON:0000072!1.85e-11!27;UBERON:0000077!4.59e-11!35;UBERON:0000063!3.37e-08!35;UBERON:0007811!6.79e-08!36;UBERON:0000065!8.84e-08!41;UBERON:0001004!1.59e-07!42
|ontology_enrichment_uberon=UBERON:0002384!3.79e-14!46;UBERON:0002193!5.12e-14!48;UBERON:0002405!5.12e-14!48;UBERON:0002370!5.90e-14!23;UBERON:0000974!5.90e-14!23;UBERON:0004807!5.90e-14!23;UBERON:0005058!5.90e-14!23;UBERON:0003351!5.90e-14!23;UBERON:0009113!5.90e-14!23;UBERON:0003295!5.90e-14!23;UBERON:0009722!5.90e-14!23;UBERON:0005562!5.90e-14!23;UBERON:0007690!5.90e-14!23;UBERON:0002390!1.49e-13!45;UBERON:0003061!1.49e-13!45;UBERON:0006562!2.97e-13!24;UBERON:0003408!2.97e-13!24;UBERON:0001557!2.97e-13!24;UBERON:0001042!2.97e-13!24;UBERON:0008814!2.97e-13!24;UBERON:0009145!2.97e-13!24;UBERON:0004177!3.76e-12!29;UBERON:0005057!3.76e-12!29;UBERON:0000072!1.85e-11!27;UBERON:0000077!4.59e-11!35;UBERON:0000063!3.37e-08!35;UBERON:0007811!6.79e-08!36;UBERON:0000065!8.84e-08!41;UBERON:0001004!1.59e-07!42
|tfbs_overrepresentation_for_novel_motifs=0.464314,0.275767,0.183547,0.0755031,0.403653,0.586776,0.401081,0.0859655,0.580724,0.148944,0.340369,0.384124,0.188374,0.418601,0.447409,0,0.259755,0.633675,0.160901,0.17599,0.339522,0.38226,0.417302,0.399688,0.74741,0.458764,0.273327,0.306197,0.0285758,0.291087,0.288134,0.892346,0.193804,0.372412,0.448703,0.105131,0.0147176,0.379077,0.51446,0.418456,0.203128,1.02935,0.830337,0.239128,0.139102,0.248078,0.590335,1.11271,0.345469,0.289613,0.247239,0.166621,0.614824,1.14457,0.465864,0.428923,0.0317166,0.366398,0.249356,0.137352,0.85762,0.172475,0.230012,0.239273,0.44515,0.268299,0.584509,0.907487,0.849558,0.768874,0.0425289,0.357014,0.0513316,0.494514,0.0157647,0.105383,0.11583,0.572368,0.307225,0.62578,0.829399,0.272401,0.171576,0.176026,0.397678,0.150777,0.000101229,0.168746,0.207637,1.06309,0.64713,0.40175,0.34595,0.218578,0.0529479,0.441628,1.06751,0.348163,0.59074,0.125187,0.354785,0.335693,0.436484,0.247661,0.246912,0.0872264,0.290513,0.661283,0.15524,0.342885,0.449672,0.437975,0.629125,0.106977,0.653522,0.64149,0.166513,0.0771455,0.722152,0.345519,0.499163,0.638433,0.461462,1.08366,0.702969,0.310043,0.132139,0.340627,0.58316,0.223308,0.422342,0.252711,0.556974,0.880148,0.673182,0.249312,0.832351,0.296517,0.628575,1.42304,1.03234,0.588705,0.158669,0.910596,0.242322,0.295293,0.206447,1.38398,0.0625146,0.408198,0.0872909,0.00084391,0.452434,0.0465279,0.145874,0.522448,0.500553,0.479846,0.209338,0.481369,0.637161,0.396979,0.835186,0.445014,0.674221,0.859524,0.587533,0.381906,0.26753
}}
}}

Revision as of 18:04, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:59837508..59837512,+p@chr10:59837508..59837512
+
Mm9::chr10:61969030..61969043,-p@chr10:61969030..61969043
-
Mm9::chr11:70464139..70464152,+p@chr11:70464139..70464152
+
Mm9::chr11:82877968..82877973,+p@chr11:82877968..82877973
+
Mm9::chr11:82877992..82878000,+p@chr11:82877992..82878000
+
Mm9::chr15:78402228..78402241,+p@chr15:78402228..78402241
+
Mm9::chr17:21587400..21587411,+p@chr17:21587400..21587411
+
Mm9::chr17:35399747..35399768,+p3@H2-D1
Mm9::chr1:163001536..163001548,-p@chr1:163001536..163001548
-
Mm9::chr1:58770164..58770176,+p4@Cflar
Mm9::chr1:92949614..92949625,-p@chr1:92949614..92949625
-
Mm9::chr1:92950423..92950427,-p@chr1:92950423..92950427
-
Mm9::chr1:92950550..92950569,+p@chr1:92950550..92950569
+
Mm9::chr1:92953199..92953213,+p@chr1:92953199..92953213
+
Mm9::chr1:92953250..92953273,+p@chr1:92953250..92953273
+
Mm9::chr1:92954465..92954475,+p@chr1:92954465..92954475
+
Mm9::chr2:73301971..73301982,-p@chr2:73301971..73301982
-
Mm9::chr2:73323739..73323761,-p12@Wipf1
Mm9::chr2:94278218..94278232,-p2@Api5
Mm9::chr4:8840833..8840836,-p@chr4:8840833..8840836
-
Mm9::chr5:108155037..108155060,-p2@Gfi1
Mm9::chr5:32000704..32000714,-p@chr5:32000704..32000714
-
Mm9::chr5:32436063..32436081,+p@chr5:32436063..32436081
+
Mm9::chr5:32436178..32436190,+p@chr5:32436178..32436190
+
Mm9::chr7:109398056..109398073,-p@chr7:109398056..109398073
-
Mm9::chr7:31203177..31203188,+p@chr7:31203177..31203188
+
Mm9::chr7:31204934..31204968,+p@chr7:31204934..31204968
+
Mm9::chr7:31205383..31205392,-p@chr7:31205383..31205392
-
Mm9::chr7:31206627..31206655,-p@chr7:31206627..31206655
-
Mm9::chr8:129376078..129376081,-p@chr8:129376078..129376081
-
Mm9::chr8:85856266..85856269,-p3@Elmod2
Mm9::chr9:66767453..66767517,-p1@Rab8b


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:0042660positive regulation of cell fate specification0.0327773654156251
GO:0042659regulation of cell fate specification0.0327773654156251
GO:0010453regulation of cell fate commitment0.0327773654156251
GO:0009996negative regulation of cell fate specification0.0327773654156251
GO:0010454negative regulation of cell fate commitment0.0327773654156251
GO:0043154negative regulation of caspase activity0.0382809443418322
GO:0007638mechanosensory behavior0.0382809443418322
GO:0043066negative regulation of apoptosis0.0382809443418322
GO:0043069negative regulation of programmed cell death0.0382809443418322
GO:0005522profilin binding0.0491283492655764



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>disease_data<br>

Cell Type
Ontology termp-valuen
lymphoid lineage restricted progenitor cell5.43e-2312
mature alpha-beta T cell1.30e-219
alpha-beta T cell1.30e-219
immature T cell1.30e-219
mature T cell1.30e-219
immature alpha-beta T cell1.30e-219
lymphocyte4.99e-2113
common lymphoid progenitor4.99e-2113
T cell5.39e-2111
pro-T cell5.39e-2111
hematopoietic cell5.26e-2032
hematopoietic oligopotent progenitor cell5.26e-2032
hematopoietic stem cell5.26e-2032
angioblastic mesenchymal cell5.26e-2032
hematopoietic multipotent progenitor cell5.26e-2032
CD4-positive, alpha-beta T cell2.13e-198
nucleate cell1.30e-1616
leukocyte1.73e-1517
nongranular leukocyte1.73e-1517
thymocyte5.39e-156
double negative thymocyte5.39e-156
naive T cell5.39e-156
double-positive, alpha-beta thymocyte5.39e-156
CD4-positive, alpha-beta thymocyte5.39e-156
naive thymus-derived CD4-positive, alpha-beta T cell5.39e-156
DN4 thymocyte5.39e-156
DN1 thymic pro-T cell5.39e-156
DN2 thymocyte5.39e-156
DN3 thymocyte5.39e-156
immature single positive thymocyte5.39e-156
early T lineage precursor5.39e-156
mature CD4 single-positive thymocyte5.39e-156
resting double-positive thymocyte5.39e-156
double-positive blast5.39e-156
CD69-positive double-positive thymocyte5.39e-156
CD69-positive, CD4-positive single-positive thymocyte5.39e-156
CD4-positive, CD8-intermediate double-positive thymocyte5.39e-156
CD24-positive, CD4 single-positive thymocyte5.39e-156
connective tissue cell3.79e-1446
mesenchymal cell3.79e-1446
hematopoietic lineage restricted progenitor cell1.37e-1325
motile cell1.05e-1254
stem cell1.15e-0997
somatic stem cell1.32e-0791
multi fate stem cell1.32e-0791

Uber Anatomy
Ontology termp-valuen
connective tissue3.79e-1446
hemolymphoid system5.12e-1448
immune system5.12e-1448
thymus5.90e-1423
neck5.90e-1423
respiratory system epithelium5.90e-1423
hemolymphoid system gland5.90e-1423
pharyngeal epithelium5.90e-1423
thymic region5.90e-1423
pharyngeal gland5.90e-1423
entire pharyngeal arch endoderm5.90e-1423
thymus primordium5.90e-1423
early pharyngeal endoderm5.90e-1423
hematopoietic system1.49e-1345
blood island1.49e-1345
pharynx2.97e-1324
gland of gut2.97e-1324
upper respiratory tract2.97e-1324
chordate pharynx2.97e-1324
pharyngeal arch system2.97e-1324
pharyngeal region of foregut2.97e-1324
hemopoietic organ3.76e-1229
immune organ3.76e-1229
segment of respiratory tract1.85e-1127
mixed endoderm/mesoderm-derived structure4.59e-1135
organ segment3.37e-0835
craniocervical region6.79e-0836
respiratory tract8.84e-0841
respiratory system1.59e-0742

Disease
Ontology termp-valuen
musculoskeletal system cancer1.69e-083
muscle cancer1.69e-083


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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