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Coexpression cluster:C2371: Difference between revisions

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{{Coexpression_clusters
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486914,0.175784,0.262778,0.373453,0.362662,0.433518,0.184359,0.334474,0.325785,0.257476,0.291176,0.376537,0.322827,0.229571,0.359036,0.335984,0.171704,0.208256,0.265058,0.256405,0.362898,0.302133,0.40806,0.151361,0.279606,0.286696,0.150674,0.251128,0.246177,0.35674,0.35852,0.318525,0.213257,0.287217,0.122782,0.410951,0.289049,0.266974,0.125746,0.112897,0.398354,0.222091,0.205977,0.34423,0.0936726,0.343425,0.132374,0.285122,0.22741,0.203996,0.276721,0.321965,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,0.392841,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,1.53003,0.892087,0.316693,1.72987,0.537869,0.806311,0.682839,1.09415,0.433165,1.63198,0.49475,0.285913,0.491074,0.740899,2.0411,0.371755,0.493145,0.66492,0.539378,0.53106,0.314427,0.61613,1.92371,0.694903,1.57574,0.538016,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,0.806003,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,4.10155,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,0.12452,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,2.16698,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,1.58937,0.437774,1.23342,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,1.47036,0.997702,1.96584,1.90479,0.820225,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;0.0938548,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;1.41335,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;2.52375,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;0.824639,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;1.98521,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;5.61029,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.380957,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.02755,MA0089.1;0,MA0090.1;3.80961,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;4.54044,MA0103.1;0.521546,MA0105.1;2.66951,MA0106.1;0.869173,MA0107.1;6.4056,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;1.98562,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;1.46638,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;1.13403,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;3.22574,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;1.02191,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;2.03616,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.253219,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;4.78886,MA0099.2;0.7872,MA0079.2;2.35343,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2371_Renal_Lymphatic_Alveolar_migratory_Endothelial_heart_tongue
|id=C2371
}}

Latest revision as of 12:04, 17 September 2013


Full id: C2371_Renal_Lymphatic_Alveolar_migratory_Endothelial_heart_tongue



Phase1 CAGE Peaks

Hg19::chr16:3115299..3115312,+p5@IL32
Hg19::chr16:3115324..3115364,+p3@IL32
Hg19::chr16:3115386..3115412,+p2@IL32
Hg19::chr16:3115418..3115429,+p4@IL32


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

No GOStat results

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
epithelial tube8.39e-32117
vessel2.97e-2268
unilaminar epithelium8.16e-21148
mesenchyme5.76e-20160
entire embryonic mesenchyme5.76e-20160
splanchnic layer of lateral plate mesoderm8.47e-2083
epithelial tube open at both ends1.55e-1759
blood vessel1.55e-1759
blood vasculature1.55e-1759
vascular cord1.55e-1759
anatomical conduit1.66e-17240
vasculature3.21e-1778
vascular system3.21e-1778
trunk3.69e-17199
trunk mesenchyme4.24e-17122
circulatory system7.65e-17112
cardiovascular system4.48e-16109
organism subdivision3.47e-14264
abdominal segment of trunk6.18e-1460
abdomen6.18e-1460
abdomen element9.14e-1454
abdominal segment element9.14e-1454
epithelium9.52e-14306
cell layer3.26e-13309
compound organ5.77e-1368
tube1.37e-12192
anatomical cluster1.92e-12373
artery1.11e-1142
arterial blood vessel1.11e-1142
arterial system1.11e-1142
gut epithelium1.89e-1054
subdivision of trunk2.76e-10112
systemic artery4.95e-1033
systemic arterial system4.95e-1033
multi-tissue structure9.96e-10342
renal system2.09e-0948
urinary system structure3.37e-0947
trunk region element3.67e-09101
nephron epithelium4.21e-0915
renal tubule4.21e-0915
nephron tubule4.21e-0915
nephron4.21e-0915
uriniferous tubule4.21e-0915
nephrogenic mesenchyme4.21e-0915
parenchyma4.31e-0915
excretory tube4.89e-0916
kidney epithelium4.89e-0916
multilaminar epithelium5.47e-0983
epithelial vesicle6.86e-0978
muscle tissue1.06e-0864
musculature1.06e-0864
musculature of body1.06e-0864
skeletal muscle tissue2.27e-0862
striated muscle tissue2.27e-0862
myotome2.27e-0862
endo-epithelium3.66e-0882
immaterial anatomical entity4.07e-08117
blood vessel endothelium4.08e-0818
endothelium4.08e-0818
cardiovascular system endothelium4.08e-0818
epithelium of foregut-midgut junction1.17e-0725
anatomical boundary1.17e-0725
hepatobiliary system1.17e-0725
foregut-midgut junction1.17e-0725
septum transversum1.17e-0725
cortex of kidney1.78e-0712
renal parenchyma1.78e-0712
liver2.09e-0719
digestive gland2.09e-0719
liver bud2.09e-0719
aorta2.10e-0721
aortic system2.10e-0721
digestive tract diverticulum3.20e-0723
hepatic diverticulum3.80e-0722
liver primordium3.80e-0722
kidney5.41e-0726
kidney mesenchyme5.41e-0726
upper urinary tract5.41e-0726
kidney rudiment5.41e-0726


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.11.41335
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.12.52375
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.15.61029
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.380957
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.02755
MA0089.10
MA0090.13.80961
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.14.54044
MA0103.10.521546
MA0105.12.66951
MA0106.10.869173
MA0107.16.4056
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.11.46638
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.21.13403
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.23.22574
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.12.03616
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.24.78886
MA0099.20.7872
MA0079.22.35343
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
EP300#203346.77394172622320.0004748459821442640.00433879610928826
FOSL2#2355416.93020060456171.2165416097647e-050.00030330482020104
HDAC2#3066413.41562023662633.0859005065161e-050.00062616740431326
HEY1#2346244.040111043105710.00375304636917980.0185835582093101
HNF4A#3172423.13229036295373.48990320893214e-060.000115452011795269
HNF4G#3174428.75342252644681.46167379934821e-065.66230526447062e-05
HSF1#32974164.2906666666671.36534966436082e-091.22715794833201e-07
JUN#3725412.51282919233634.07770316866756e-050.000742582809472487
JUND#372746.994663941871030.000417684217818580.00391338674304788
NFKB1#479045.488063424193840.001102199566301980.0076751980600755
PPARGC1A#108914350.0511363636366.58479147384085e-117.28505335525915e-09
RXRA#6256420.07461713913336.1537798808435e-060.00018211805524948
SIN3A#2594245.408884726815140.001168172384885160.00795531792547084
SP1#666745.69838137814090.0009482606065333980.0068370997228679
TCF12#6938410.63446490218647.8163066689251e-050.00119977550293338
ZNF263#1012736.166381227758010.006539814347975980.0279670653790952



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

This analysis result is provided for C0 - C305 clusters.

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