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{{Coexpression_clusters
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9,0.00481597,6.94316e-14,0.000602298,0.00915113,0.00205547,5.66171e-10,0.000128601,0.0192184,0.0103319,2.82032e-08,0.0927631,0.167977,0.00825845,0.0185729,0.00569792,3.95255e-06,0.00562987,0.0783957,0.0474704,2.63376e-05,0.0438303,0.0112518,0.0350451,0.220779,0.494601,0.0601209,0.365091,0.00106395,2.7677e-06,1.13254e-09,0.166856,1.83496e-07,8.81747e-08,3.86643e-08,0.0393653,0.0590566,0.000713981,6.17787e-05,0.043538,0.0112126,0.000210646,0.139208,4.96629e-15,1.54015e-10,1.8315e-08,0.0237156,1.41691,0.282893,0.125652,0.0694567,0.000696363,0.000120713,0.00102185,6.29654e-06,0.0856203,0.0245782,0.000126974,0.000226457,0.0674527,0.0833978,0.195891,0.131359,0.00226014,0.0481962,0.00770414,0.000797129,7.75451e-05,0.0032486,0.0823066,0.000282674,0.00276777,0.2502,0.00040736,2.02509e-15,0.00170125,0.0344919,0.0216532,0.162248,0.0232695,0.00354855,0.0125119,0.327738,0.0395599,0.0435604,0.071255,0.547652,1.66792e-05,0.12599,0.0118884,0.195121,0.157386,0.291918,1.13677e-08,0.00157632,0.0032454,0.262584,0.995421,0.62471,0.237778,0.00861535,0.0842115,0.0327738,0.00514507,0.120466,0.845442,0.00125939,9.00694e-06,9.42434e-09,1.97012e-12,0.126177,1.8549e-05,0.00933292,0.388619,0.228987,0.00381235,0.000801721,0.000457704,0.236987,0.117257,0.213463,0.000488681,0.0365694,0.0111253,0.000429301,0.00892117,2.96049e-14|tfbs_overrepresentation_jaspar=MA0003.1;0,MA0004.1;0.00260673,MA0006.1;0.000112973,MA0007.1;0.00196851,MA0009.1;0.106476,MA0014.1;0,MA0017.1;0.000292928,MA0019.1;0.0145471,MA0024.1;0.0644828,MA0025.1;0.175475,MA0027.1;1.46439,MA0028.1;0.000169921,MA0029.1;0.0713631,MA0030.1;0.0672343,MA0031.1;0.0465722,MA0038.1;0.0471975,MA0040.1;0.255982,MA0041.1;0.0202287,MA0042.1;0.0459162,MA0043.1;0.106619,MA0046.1;0.333015,MA0048.1;1.88169e-09,MA0050.1;0.00216419,MA0051.1;0.00890693,MA0052.1;0.0749729,MA0055.1;1.65593e-11,MA0056.1;0,MA0057.1;2.38167e-08,MA0058.1;0.000502429,MA0059.1;0.00048935,MA0060.1;2.62107e-05,MA0061.1;5.29141e-07,MA0063.1;0,MA0066.1;0.00935718,MA0067.1;0.294478,MA0068.1;8.34177e-06,MA0069.1;0.0998855,MA0070.1;0.650463,MA0071.1;0.00603941,MA0072.1;0.093111,MA0073.1;0,MA0074.1;0.00883558,MA0076.1;0.000688379,MA0077.1;0.0898728,MA0078.1;0.0223541,MA0081.1;0.000490982,MA0083.1;0.109916,MA0084.1;0.43698,MA0087.1;0.0920771,MA0088.1;1.02593e-10,MA0089.1;0,MA0090.1;0.000902456,MA0091.1;0.00270748,MA0092.1;0.00151369,MA0093.1;0.00112333,MA0095.1;0,MA0098.1;0,MA0100.1;0.0107507,MA0101.1;0.000133124,MA0103.1;0.00404296,MA0105.1;3.54892e-10,MA0106.1;0.0140309,MA0107.1;1.45596e-05,MA0108.2;0.0457009,MA0109.1;0,MA0111.1;0.00114851,MA0113.1;0.0162992,MA0114.1;0.000139462,MA0115.1;0.242118,MA0116.1;1.64375e-05,MA0117.1;0.124249,MA0119.1;0.000348463,MA0122.1;0.137275,MA0124.1;0.21537,MA0125.1;0.165293,MA0130.1;0,MA0131.1;0.0257778,MA0132.1;0,MA0133.1;0,MA0135.1;0.383334,MA0136.1;0.0100269,MA0139.1;3.19704e-05,MA0140.1;0.00585093,MA0141.1;0.0037082,MA0142.1;0.0380114,MA0143.1;0.0163249,MA0144.1;7.12455e-06,MA0145.1;1.52722e-11,MA0146.1;1.03566e-08,MA0147.1;1.85409e-05,MA0148.1;0.00369235,MA0149.1;0.0052018,MA0062.2;3.99669e-07,MA0035.2;0.00580167,MA0039.2;0,MA0138.2;0.0225756,MA0002.2;1.58492e-05,MA0137.2;0.00173079,MA0104.2;1.90353e-06,MA0047.2;0.0125001,MA0112.2;1.82439e-10,MA0065.2;5.32925e-08,MA0150.1;0.000809456,MA0151.1;0,MA0152.1;0.00632458,MA0153.1;0.155952,MA0154.1;6.85301e-08,MA0155.1;1.05319e-08,MA0156.1;0.000209934,MA0157.1;0.0314791,MA0158.1;0,MA0159.1;0.000209219,MA0160.1;0.00450714,MA0161.1;0,MA0162.1;3.34454e-09,MA0163.1;0,MA0164.1;0.0181753,MA0080.2;0.000122564,MA0018.2;0.0142132,MA0099.2;0.00635111,MA0079.2;0,MA0102.2;0.467262,MA0258.1;4.88472e-06,MA0259.1;2.45634e-05,MA0442.1;0}}
|full_id=C180_skeletal_heart_Hepatocyte_acute_occipital_hippocampus_middle
|gostat_on_coexpression_clusters=GO:0045298!tubulin complex!0.00417991286942188!7178$GO:0005771!multivesicular body!0.00417991286942188!7178$GO:0005770!late endosome!0.0271694336512422!7178$GO:0055074!calcium ion homeostasis!0.0271694336512422!7178$GO:0006874!cellular calcium ion homeostasis!0.0271694336512422!7178$GO:0006875!cellular metal ion homeostasis!0.0271694336512422!7178$GO:0055065!metal ion homeostasis!0.0271694336512422!7178$GO:0006916!anti-apoptosis!0.0271694336512422!7178$GO:0030005!cellular di-, tri-valent inorganic cation homeostasis!0.0271694336512422!7178$GO:0055066!di-, tri-valent inorganic cation homeostasis!0.0271694336512422!7178$GO:0006816!calcium ion transport!0.0271694336512422!7178$GO:0005768!endosome!0.0271694336512422!7178$GO:0030003!cellular cation homeostasis!0.0271694336512422!7178$GO:0055080!cation homeostasis!0.0271694336512422!7178$GO:0043066!negative regulation of apoptosis!0.0271694336512422!7178$GO:0043069!negative regulation of programmed cell death!0.0271694336512422!7178$GO:0055082!cellular chemical homeostasis!0.0271694336512422!7178$GO:0006873!cellular ion homeostasis!0.0271694336512422!7178$GO:0015674!di-, tri-valent inorganic cation transport!0.0271694336512422!7178$GO:0050801!ion homeostasis!0.027900918403391!7178$GO:0005874!microtubule!0.0286894019673956!7178$GO:0048878!chemical homeostasis!0.0286894019673956!7178$GO:0019725!cellular homeostasis!0.0340753766528957!7178$GO:0042592!homeostatic process!0.0417991286942188!7178$GO:0015630!microtubule cytoskeleton!0.0424421922125913!7178$GO:0005615!extracellular space!0.0424421922125913!7178$GO:0042981!regulation of apoptosis!0.0429933895140536!7178$GO:0043067!regulation of programmed cell death!0.0429933895140536!7178$GO:0030001!metal ion transport!0.04915000994734!7178
|id=C180
}}

Latest revision as of 10:50, 17 September 2013


Full id: C180_skeletal_heart_Hepatocyte_acute_occipital_hippocampus_middle



Phase1 CAGE Peaks

Hg19::chr11:114126059..114126109,+p@chr11:114126059..114126109
+
Hg19::chr1:160111262..160111295,+p@chr1:160111262..160111295
+
Hg19::chr1:160113171..160113182,+p@chr1:160113171..160113182
+
Hg19::chr1:569901..569922,+p1@ENST00000416718
Hg19::chr1:569934..569952,-p@chr1:569934..569952
-
Hg19::chr2:88124475..88124516,+p1@MT-ATP8
Hg19::chr3:25508993..25509011,+p@chr3:25508993..25509011
+
Hg19::chr4:8036848..8036871,-p@chr4:8036848..8036871
-
Hg19::chr5:134259184..134259218,-p@chr5:134259184..134259218
-
Hg19::chr5:134259896..134259899,+p2@MTND6P4
Hg19::chr5:134260273..134260314,-p@chr5:134260273..134260314
-
Hg19::chr5:134261636..134261669,-p1@MTND5P11
Hg19::chr5:134262765..134262773,-p@chr5:134262765..134262773
-
Hg19::chr5:134264011..134264014,-p1@MIR4461
Hg19::chr8:100508136..100508173,-p@chr8:100508136..100508173
-
Hg19::chrM:10053..10073,+p1@AB017116
Hg19::chrM:10173..10184,+p11@uc004cov.3
Hg19::chrM:10464..10480,+p1@uc004cov.3
Hg19::chrM:10568..10581,+p5@uc004cov.3
Hg19::chrM:10642..10656,+p8@uc004cov.3
Hg19::chrM:10671..10697,+p3@uc004cov.3
Hg19::chrM:10722..10734,+p7@uc004cov.3
Hg19::chrM:10741..10754,+p4@uc004cov.3
Hg19::chrM:10758..10771,+p6@uc004cov.3
Hg19::chrM:10850..10862,+p9@uc004cov.3
Hg19::chrM:10882..10893,+p12@uc004cov.3
Hg19::chrM:10902..10945,+p2@uc004cov.3
Hg19::chrM:11163..11176,+p1@AK129724
Hg19::chrM:11216..11233,+p2@AK129724
Hg19::chrM:11243..11254,+p3@Y17178
Hg19::chrM:11272..11283,+p2@Y17178
Hg19::chrM:11324..11335,+p4@Y17178
Hg19::chrM:11437..11449,+p1@Y17178
Hg19::chrM:11554..11580,-p@chrM:11554..11580
-
Hg19::chrM:11795..11807,+p1@uc004cow.1
Hg19::chrM:12331..12348,+p1@uc004cox.3
Hg19::chrM:12769..12780,+p2@uc004cox.3
Hg19::chrM:13632..13643,+p@chrM:13632..13643
+
Hg19::chrM:13938..13949,+p@chrM:13938..13949
+
Hg19::chrM:13966..13989,+p@chrM:13966..13989
+
Hg19::chrM:14077..14089,+p@chrM:14077..14089
+
Hg19::chrM:15039..15050,+p3@BC016999
Hg19::chrM:15149..15161,+p4@BC016999
Hg19::chrM:15168..15192,+p2@BC016999
Hg19::chrM:15239..15263,+p1@BC016999
Hg19::chrM:15280..15291,+p5@BC016999
Hg19::chrM:15293..15304,+p3@AF391805
Hg19::chrM:15306..15332,+p2@AF391805
Hg19::chrM:15419..15448,+p1@AF391805
Hg19::chrM:15517..15545,+p1@uc004coz.1
Hg19::chrM:15611..15622,+p3@uc004coz.1
Hg19::chrM:16098..16117,+p2@uc004coz.1
Hg19::chrM:16145..16159,+p4@uc004coz.1
Hg19::chrM:16183..16194,+p9@uc004coz.1
Hg19::chrM:16229..16242,+p10@uc004coz.1
Hg19::chrM:16274..16381,-p@chrM:16274..16381
-
Hg19::chrM:16481..16490,-p@chrM:16481..16490
-
Hg19::chrM:2028..2040,+p6@uc004cos.3
Hg19::chrM:3299..3324,+p2@TPT1
Hg19::chrM:3434..3445,+p1@AF216862
Hg19::chrM:3565..3576,+p1@AK123234
Hg19::chrM:3695..3706,+p2@AK123234
Hg19::chrM:4012..4049,+p1@M25300
Hg19::chrM:4716..4729,+p1@AK026903
Hg19::chrM:4817..4837,+p4@AF275801
Hg19::chrM:4876..4946,+p2@AF275801
Hg19::chrM:4960..4989,+p1@AF275801
Hg19::chrM:5028..5039,+p5@AF275801
Hg19::chrM:5113..5148,+p3@AF275801
Hg19::chrM:526..537,-p4@uc004coq.3
Hg19::chrM:5984..6024,+p7@uc011mfh.1
Hg19::chrM:6190..6248,+p2@uc011mfh.1
Hg19::chrM:6250..6272,+p4@uc011mfh.1
Hg19::chrM:6330..6392,+p1@uc011mfh.1
Hg19::chrM:6437..6448,+p3@AK026547
Hg19::chrM:6463..6517,+p1@AK026547
Hg19::chrM:6523..6548,+p2@AK026547
Hg19::chrM:6608..6637,+p4@AK026547
Hg19::chrM:6910..6936,+p1@BC018860
Hg19::chrM:7109..7147,+p4@uc004cou.3
Hg19::chrM:7213..7257,+p7@uc004cou.3
Hg19::chrM:7604..7655,+p1@uc004cou.3
Hg19::chrM:7678..7687,+p10@uc004cou.3
Hg19::chrM:7689..7700,+p5@uc004cou.3
Hg19::chrM:7772..7783,+p11@uc004cou.3
Hg19::chrM:7787..7811,+p3@uc004cou.3
Hg19::chrM:7840..7897,+p2@uc004cou.3
Hg19::chrM:7993..8026,+p6@uc004cou.3
Hg19::chrM:8423..8463,+p1@uc011mfi.1
Hg19::chrM:8512..8534,-p@chrM:8512..8534
-
Hg19::chrM:8630..8675,+p2@uc011mfi.1
Hg19::chrM:8717..8734,-p4@AF271776
Hg19::chrM:9226..9255,+p1@AL359334
p1@L08441
Hg19::chrM:9538..9549,+p2@BC023992
Hg19::chrX:125606790..125606809,+p1@MTND4P24


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

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0045298tubulin complex0.00417991286942188
GO:0005771multivesicular body0.00417991286942188
GO:0005770late endosome0.0271694336512422
GO:0055074calcium ion homeostasis0.0271694336512422
GO:0006874cellular calcium ion homeostasis0.0271694336512422
GO:0006875cellular metal ion homeostasis0.0271694336512422
GO:0055065metal ion homeostasis0.0271694336512422
GO:0006916anti-apoptosis0.0271694336512422
GO:0030005cellular di-, tri-valent inorganic cation homeostasis0.0271694336512422
GO:0055066di-, tri-valent inorganic cation homeostasis0.0271694336512422
GO:0006816calcium ion transport0.0271694336512422
GO:0005768endosome0.0271694336512422
GO:0030003cellular cation homeostasis0.0271694336512422
GO:0055080cation homeostasis0.0271694336512422
GO:0043066negative regulation of apoptosis0.0271694336512422
GO:0043069negative regulation of programmed cell death0.0271694336512422
GO:0055082cellular chemical homeostasis0.0271694336512422
GO:0006873cellular ion homeostasis0.0271694336512422
GO:0015674di-, tri-valent inorganic cation transport0.0271694336512422
GO:0050801ion homeostasis0.027900918403391
GO:0005874microtubule0.0286894019673956
GO:0048878chemical homeostasis0.0286894019673956
GO:0019725cellular homeostasis0.0340753766528957
GO:0042592homeostatic process0.0417991286942188
GO:0015630microtubule cytoskeleton0.0424421922125913
GO:0005615extracellular space0.0424421922125913
GO:0042981regulation of apoptosis0.0429933895140536
GO:0043067regulation of programmed cell death0.0429933895140536
GO:0030001metal ion transport0.04915000994734



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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
neural tube1.81e-2056
neural rod1.81e-2056
future spinal cord1.81e-2056
neural keel1.81e-2056
adult organism2.50e-20114
regional part of nervous system5.20e-1953
regional part of brain5.20e-1953
nervous system2.55e-1789
central nervous system3.19e-1781
regional part of forebrain5.83e-1741
forebrain5.83e-1741
anterior neural tube5.83e-1741
future forebrain5.83e-1741
brain1.28e-1568
future brain1.28e-1568
brain grey matter1.07e-1434
gray matter1.07e-1434
telencephalon9.46e-1434
neurectoderm1.60e-1386
regional part of telencephalon1.83e-1332
cerebral hemisphere3.63e-1332
neural plate5.10e-1382
presumptive neural plate5.10e-1382
regional part of cerebral cortex8.68e-1222
neocortex1.53e-1020
ecto-epithelium4.80e-10104
cerebral cortex1.16e-0925
pallium1.16e-0925
pre-chordal neural plate3.79e-0961
organ system subdivision1.42e-08223
ectoderm-derived structure8.59e-08171
ectoderm8.59e-08171
presumptive ectoderm8.59e-08171
neural nucleus8.26e-079
nucleus of brain8.26e-079
basal ganglion8.82e-079
nuclear complex of neuraxis8.82e-079
aggregate regional part of brain8.82e-079
collection of basal ganglia8.82e-079
cerebral subcortex8.82e-079
Disease
Ontology termp-valuen
disease of cellular proliferation5.35e-16239
cancer3.60e-15235
organ system cancer1.72e-08137
cell type cancer2.53e-08143


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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
MA0004.10.00260673
MA0006.10.000112973
MA0007.10.00196851
MA0009.10.106476
MA0014.10
MA0017.10.000292928
MA0019.10.0145471
MA0024.10.0644828
MA0025.10.175475
MA0027.11.46439
MA0028.10.000169921
MA0029.10.0713631
MA0030.10.0672343
MA0031.10.0465722
MA0038.10.0471975
MA0040.10.255982
MA0041.10.0202287
MA0042.10.0459162
MA0043.10.106619
MA0046.10.333015
MA0048.11.88169e-09
MA0050.10.00216419
MA0051.10.00890693
MA0052.10.0749729
MA0055.11.65593e-11
MA0056.10
MA0057.12.38167e-08
MA0058.10.000502429
MA0059.10.00048935
MA0060.12.62107e-05
MA0061.15.29141e-07
MA0063.10
MA0066.10.00935718
MA0067.10.294478
MA0068.18.34177e-06
MA0069.10.0998855
MA0070.10.650463
MA0071.10.00603941
MA0072.10.093111
MA0073.10
MA0074.10.00883558
MA0076.10.000688379
MA0077.10.0898728
MA0078.10.0223541
MA0081.10.000490982
MA0083.10.109916
MA0084.10.43698
MA0087.10.0920771
MA0088.11.02593e-10
MA0089.10
MA0090.10.000902456
MA0091.10.00270748
MA0092.10.00151369
MA0093.10.00112333
MA0095.10
MA0098.10
MA0100.10.0107507
MA0101.10.000133124
MA0103.10.00404296
MA0105.13.54892e-10
MA0106.10.0140309
MA0107.11.45596e-05
MA0108.20.0457009
MA0109.10
MA0111.10.00114851
MA0113.10.0162992
MA0114.10.000139462
MA0115.10.242118
MA0116.11.64375e-05
MA0117.10.124249
MA0119.10.000348463
MA0122.10.137275
MA0124.10.21537
MA0125.10.165293
MA0130.10
MA0131.10.0257778
MA0132.10
MA0133.10
MA0135.10.383334
MA0136.10.0100269
MA0139.13.19704e-05
MA0140.10.00585093
MA0141.10.0037082
MA0142.10.0380114
MA0143.10.0163249
MA0144.17.12455e-06
MA0145.11.52722e-11
MA0146.11.03566e-08
MA0147.11.85409e-05
MA0148.10.00369235
MA0149.10.0052018
MA0062.23.99669e-07
MA0035.20.00580167
MA0039.20
MA0138.20.0225756
MA0002.21.58492e-05
MA0137.20.00173079
MA0104.21.90353e-06
MA0047.20.0125001
MA0112.21.82439e-10
MA0065.25.32925e-08
MA0150.10.000809456
MA0151.10
MA0152.10.00632458
MA0153.10.155952
MA0154.16.85301e-08
MA0155.11.05319e-08
MA0156.10.000209934
MA0157.10.0314791
MA0158.10
MA0159.10.000209219
MA0160.10.00450714
MA0161.10
MA0162.13.34454e-09
MA0163.10
MA0164.10.0181753
MA0080.20.000122564
MA0018.20.0142132
MA0099.20.00635111
MA0079.20
MA0102.20.467262
MA0258.14.88472e-06
MA0259.12.45634e-05
MA0442.10



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

No analysis results for this cluster

Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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