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Coexpression cluster:C2833: Difference between revisions

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{{Coexpression_clusters
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028353,0.000378293,0.259989,0.390754,0.355805,0.000372103,0.108118,0.259901,0.0102507,0.0708274,0.0710478,0.196248,0.102645,0.0539258,0.0709978,0.401939,0.0627853,0.271338,0.032013,0.298673,0.244395,0.106889,0.128632,0.0845989,0.0133959,0.0842401,0.00984212,0.0874421,0.100355,0.167854,0.142846,0.00173808,0.088258,0.117657,0.0486914,0.175784,1.70389e-05,0.373453,0.0109087,0.433518,0.184359,0.0634867,0.325785,0.257476,0.0472356,1.03222e-05,0.0588457,1.29683e-08,0.0739466,0.000845912,0.171704,0.00178316,0.265058,0.0361085,7.93582e-06,0.302133,0.0163014,0.0120812,0.279606,0.00499935,0.150674,0.251128,0.246177,0.35674,0.00113802,0.0571822,0.213257,0.287217,0.122782,0.0991993,0.289049,0.266974,0.125746,0.112897,0.398354,0.00218951,0.205977,0.34423,0.0936726,0.343425,0.132374,0.045178,0.00236186,0.00166967,0.276721,5.34722e-05,0.264707,0.450113|tfbs_overrepresentation_for_novel_motifs=0.590005,0.298605,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.80003,0.902371,2.82941,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.223552,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,8.28911,0.491074,0.740899,0.463978,1.72725,0.493145,0.66492,0.183156,0.53106,0.0946706,0.61613,0.822818,1.65941,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,2.26787,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,0.321165,0.305238,1.00941,1.08,0.62601,0.362435,2.33882,0.844168,0.399165,1.27559,0.353274,0.221873,2.2083,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,1.15724,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,1.52945,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.12452,0.681522,2.26288,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,14.4202,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,1.811,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.0401987|tfbs_overrepresentation_jaspar=MA0003.1;0.0214529,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;2.4142,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,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;1.28333,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.01899,MA0061.1;0.946082,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;0.100363,MA0074.1;0.819248,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;6.20284,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;0.182167,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.656404,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;2.35545,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;2.44319,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;3.05944,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.061409,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.229241,MA0155.1;0.180766,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;6.45898,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0}}
|full_id=C2833_Mesenchymal_Fibroblast_small_Pericytes_ductal_alveolar_lung
|id=C2833
}}

Latest revision as of 12:13, 17 September 2013


Full id: C2833_Mesenchymal_Fibroblast_small_Pericytes_ductal_alveolar_lung



Phase1 CAGE Peaks

Hg19::chr5:92918894..92918912,+p2@NR2F1
Hg19::chr5:92918919..92918942,+p1@NR2F1
Hg19::chr5:92918956..92918969,+p4@NR2F1
Hg19::chr5:92919312..92919334,+p13@NR2F1


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>

Cell Type
Ontology termp-valuen
mesodermal cell1.78e-10121
contractile cell1.50e-0759
muscle precursor cell8.83e-0758
myoblast8.83e-0758
multi-potent skeletal muscle stem cell8.83e-0758
Uber Anatomy
Ontology termp-valuen
anatomical cluster1.13e-33373
cell layer1.83e-28309
epithelium3.28e-27306
multi-tissue structure6.74e-27342
anatomical conduit3.85e-24240
tube1.18e-22192
structure with developmental contribution from neural crest2.72e-21132
neural plate7.94e-2182
presumptive neural plate7.94e-2182
neurectoderm9.19e-2086
central nervous system2.19e-1881
multi-cellular organism1.05e-17656
organ system subdivision1.97e-17223
neural tube2.22e-1756
neural rod2.22e-1756
future spinal cord2.22e-1756
neural keel2.22e-1756
nervous system1.65e-1689
brain2.03e-1668
future brain2.03e-1668
regional part of nervous system1.23e-1553
regional part of brain1.23e-1553
ecto-epithelium1.26e-14104
pre-chordal neural plate1.83e-1461
anatomical system3.74e-14624
organ part5.28e-14218
anatomical group7.02e-14625
organism subdivision1.10e-13264
ectoderm-derived structure1.22e-13171
ectoderm1.22e-13171
presumptive ectoderm1.22e-13171
embryo4.18e-13592
mesenchyme1.28e-12160
entire embryonic mesenchyme1.28e-12160
developing anatomical structure2.06e-12581
germ layer5.31e-12560
germ layer / neural crest5.31e-12560
embryonic tissue5.31e-12560
presumptive structure5.31e-12560
germ layer / neural crest derived structure5.31e-12560
epiblast (generic)5.31e-12560
unilaminar epithelium1.18e-11148
embryonic structure1.43e-11564
trunk1.79e-11199
regional part of forebrain4.30e-1141
forebrain4.30e-1141
anterior neural tube4.30e-1141
future forebrain4.30e-1141
trunk mesenchyme5.91e-11122
brain grey matter2.30e-1034
gray matter2.30e-1034
adult organism3.20e-10114
telencephalon5.46e-1034
regional part of telencephalon1.09e-0932
organ1.66e-09503
cerebral hemisphere2.21e-0932
epithelial tube2.67e-09117
vasculature5.26e-0978
vascular system5.26e-0978
cerebral cortex1.07e-0825
pallium1.07e-0825
posterior neural tube6.24e-0815
chordal neural plate6.24e-0815
organ segment1.52e-0798
regional part of cerebral cortex1.68e-0722
primordium2.16e-07160
epithelial vesicle4.33e-0778
subdivision of trunk4.97e-07112
neocortex8.14e-0720
vasculature of organ8.62e-0711


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)
MA0003.10.0214529
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.12.4142
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
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
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.11.01899
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.16.20284
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.656404
MA0106.10.869173
MA0107.10.453492
MA0108.22.35545
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.11.98562
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.12.44319
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
MA0140.13.05944
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.229241
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.26.45898
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#203335.08045629466740.01144298405398240.0419169377297838
FOXA1#316938.311064812039090.002740138182109850.0150413797751167
FOXA2#3170212.31523187633260.009361916285467240.0353526837667829
GATA1#2623310.17023110785030.001515158168498270.0096677421774066
GATA2#262439.55869880016550.001818151618357440.0109060902228265
GTF2F1#296239.554745657568240.001820362319304780.0109036946699858
HDAC2#3066413.41562023662633.0859005065161e-050.000628119982459628
HEY1#2346244.040111043105710.00375304636917980.0186525368683149
HNF4A#3172423.13229036295373.48990320893214e-060.000115818875512445
HNF4G#3174321.56506689483510.0001638032421292610.00203732842738333
JUND#372746.994663941871030.000417684217818580.00392394729016413
MXI1#460149.96157162875930.0001015224754950450.00142723190445914
PRDM1#639398.87321683309561.73225752892158e-066.52652395609817e-05
REST#597837.237521537096020.004104697304192610.0195919053860688
RFX5#599339.035933120396320.002144561191324070.0123900993671901
RXRA#6256315.055962854350.0004758307997303580.00434057934256607
SIN3A#2594245.408884726815140.001168172384885160.00797872969099606
SP1#666745.69838137814090.0009482606065333980.00685603250160897
SRF#6722310.34788369662590.001439893778401260.00924113969903824
TAL1#6886322.40146250808020.0001462756395930170.0018897676303136
TCF7L2#693438.077632422353010.002978381685834620.0158703675962695
TRIM28#10155313.94289378394690.0005972858184258420.0049975912186009
ZNF263#1012748.221841637010680.0002187871180958320.00249834986079276
ZZZ3#260094239.4132124352333.02023811776815e-103.05353967842776e-08



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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