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Coexpression cluster:C1091: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003081!6.56e-22!216;UBERON:0002204!2.26e-19!167;UBERON:0000926!6.97e-19!448;UBERON:0004120!6.97e-19!448;UBERON:0006603!6.97e-19!448;UBERON:0002049!5.81e-16!79;UBERON:0007798!5.81e-16!79;UBERON:0000055!1.19e-14!69;UBERON:0004535!1.30e-14!110;UBERON:0001981!3.19e-14!60;UBERON:0007500!3.19e-14!60;UBERON:0004537!3.19e-14!60;UBERON:0006965!3.19e-14!60;UBERON:0000914!5.28e-14!83;UBERON:0002329!5.28e-14!83;UBERON:0003077!5.28e-14!83;UBERON:0003059!5.28e-14!83;UBERON:0007282!5.28e-14!83;UBERON:0009618!5.28e-14!83;UBERON:0007285!5.28e-14!83;UBERON:0001009!9.58e-14!113;UBERON:0001637!1.95e-13!42;UBERON:0003509!1.95e-13!42;UBERON:0004572!1.95e-13!42;UBERON:0004872!3.37e-13!84;UBERON:0004290!4.86e-13!70;UBERON:0000486!5.95e-13!82;UBERON:0005256!1.64e-12!143;UBERON:0000468!6.70e-11!659;UBERON:0002385!1.34e-10!63;UBERON:0001015!1.34e-10!63;UBERON:0000383!1.34e-10!63;UBERON:0001134!1.36e-10!61;UBERON:0002036!1.36e-10!61;UBERON:0003082!1.36e-10!61;UBERON:0004573!5.23e-10!33;UBERON:0004571!5.23e-10!33;UBERON:0000467!1.80e-09!625;UBERON:0003914!1.90e-09!118;UBERON:0000480!3.31e-09!626;UBERON:0002371!1.44e-08!80;UBERON:0004765!1.58e-08!101;UBERON:0001434!1.58e-08!101;UBERON:0000490!4.52e-08!138;UBERON:0002193!1.85e-07!112;UBERON:0000922!1.88e-07!612;UBERON:0002384!2.02e-07!375;UBERON:0002050!2.18e-07!605;UBERON:0005423!2.18e-07!605;UBERON:0001474!2.21e-07!86;UBERON:0000923!2.57e-07!604;UBERON:0005291!2.57e-07!604;UBERON:0006598!2.57e-07!604;UBERON:0002532!2.57e-07!604;UBERON:0002100!7.93e-07!216
|ontology_enrichment_uberon=UBERON:0003081!6.56e-22!216;UBERON:0002204!2.26e-19!167;UBERON:0000926!6.97e-19!448;UBERON:0004120!6.97e-19!448;UBERON:0006603!6.97e-19!448;UBERON:0002049!5.81e-16!79;UBERON:0007798!5.81e-16!79;UBERON:0000055!1.19e-14!69;UBERON:0004535!1.30e-14!110;UBERON:0001981!3.19e-14!60;UBERON:0007500!3.19e-14!60;UBERON:0004537!3.19e-14!60;UBERON:0006965!3.19e-14!60;UBERON:0000914!5.28e-14!83;UBERON:0002329!5.28e-14!83;UBERON:0003077!5.28e-14!83;UBERON:0003059!5.28e-14!83;UBERON:0007282!5.28e-14!83;UBERON:0009618!5.28e-14!83;UBERON:0007285!5.28e-14!83;UBERON:0001009!9.58e-14!113;UBERON:0001637!1.95e-13!42;UBERON:0003509!1.95e-13!42;UBERON:0004572!1.95e-13!42;UBERON:0004872!3.37e-13!84;UBERON:0004290!4.86e-13!70;UBERON:0000486!5.95e-13!82;UBERON:0005256!1.64e-12!143;UBERON:0000468!6.70e-11!659;UBERON:0002385!1.34e-10!63;UBERON:0001015!1.34e-10!63;UBERON:0000383!1.34e-10!63;UBERON:0001134!1.36e-10!61;UBERON:0002036!1.36e-10!61;UBERON:0003082!1.36e-10!61;UBERON:0004573!5.23e-10!33;UBERON:0004571!5.23e-10!33;UBERON:0000467!1.80e-09!625;UBERON:0003914!1.90e-09!118;UBERON:0000480!3.31e-09!626;UBERON:0002371!1.44e-08!80;UBERON:0004765!1.58e-08!101;UBERON:0001434!1.58e-08!101;UBERON:0000490!4.52e-08!138;UBERON:0002193!1.85e-07!112;UBERON:0000922!1.88e-07!612;UBERON:0002384!2.02e-07!375;UBERON:0002050!2.18e-07!605;UBERON:0005423!2.18e-07!605;UBERON:0001474!2.21e-07!86;UBERON:0000923!2.57e-07!604;UBERON:0005291!2.57e-07!604;UBERON:0006598!2.57e-07!604;UBERON:0002532!2.57e-07!604;UBERON:0002100!7.93e-07!216
|tf_chipseq_enrich=EGR1#1958;5:3.11761193425634:0.0105139099038836:0.0389245741386635
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38,0.398796,0.333467,5.25418e-05,0.0781888,0.313482,0.114368,0.13361,0.003872,0.0104581,0.198877,0.239159,0.372126,0.0490654,0.223838,0.141981,0.222302,0.308331,0.325601,0.038461,0.165742,0.133385,0.00480103,0.0214207,0.189558,0.081442,0.435903,0.139793,0.19465,0.142897,0.10753,0.0894806,0.100334,0.045125,0.392173,0.450361,0.125132,0.401145,0.349581,0.00378916,0.681349,0.142384,0.101821,0.151258,0.0162861,0.00544029,0.264629,0.267153,0.554314,0.0744668,0.166208,0.340579,0.10027,0.216542,0.140095,0.339551,0.541739,0.0286254,0.000293624,0.312506,0.0118737,0.00639099,0.228257,0.190339,0.0916917,0.203718,0.416086,0.0248755,0.00940389,0.33418,0.0866209,0.0626613,0.219989,0.259794,0.228423,0.121222,0.233436,0.466178,0.316293,0.193405,0.265337,0.307168,0.313275,9.50397e-10,0.0772098,0.132332,0.0324243,0.127929,0.1565,0.188908,0.230656,0.000887713,0.0881682,0.18579,0.057259,9.68743e-09,0.0260828,0.00057769,5.25046e-07,0.0458683,0.434522,0.0971332,0.354875,0.146252,0.12193,0.384175,0.154198,0.401916,0.0162635,0.179067,0.491271,0.0657682,0.0920973,0.00585766,0.40148,0.00279422,0.0371565,0.460251,0.0290517,0.263319,0.169668,0.264355,0.126386,0.0302387,0.45894,0.189069,0.000293801,0.267581,0.1766,0.495277,0.00114095,0.0973803,0.0561172,0.115553,0.13739,0.276387,0.229078,0.396303,0.255961,0.487366,0.145278,0.159951,0.190011,0.0631125,0.356502,0.0029466,0.481419,0.248532,0.652258,0.0921742,0.00567921,0.354931,0.158525,0.43239,0.348785,0.558528,0.36346,0.180408,0.226687,0.152678,0.0657756,0.00105939,0.239072,0.0108286,0.39215,0.436719,0.325366,0.152528,0.00806028,0.0638758,0.0457329,0.208355,0.0238452,0.00431178,0.272914,0.423557,1.62123e-05,0.233355,0.197579,0.000143933,0.332254,0.24444,0.189162,0.253118,0.273827,0.0667061,0.0872385,0.223866,0.0326595,0.385626,0.427353,0.202588,0.420356,0.364345,0.0187835,0.127426,0.149927,0.0415289,0.407834,0.14084,0.0342257,0.165238,1.70693e-05,0.0933565,0.0149318,0.312516,0.111737,0.00701919,0.00371676,0.34783,0.471691,0.014063,0.504402,6.88896e-05,0.786493,0.349032,0.017712,0.795749,0.117534,0.0123301,0.697643,0.000594673,0.138164,0.408236,0.00738403,0.193296,6.71144e-07,0.380149,0.53287,0.117121,0.000221544,0.0156237,0.000227458,0.0243079,0.496897,0.014806,7.71428e-05,0.0107549,0.590655,0.0124302,0.00648132,2.36882e-18,0.0644829,0.380163,0.0269285,0.22948,0.196496,0.000441813,0.0252308,0.238873,0.549112,4.07669e-05,0.524662,3.55587e-10,0.011406,3.64015e-18,0.000349564,0.0812527,1.38906e-11,0.146126,3.59683e-06,2.76595e-06,9.11749e-08,1.52168e-08,0.00206763,0.119678,6.93116e-11,0.000238787,0.454729,0.120814,0.458665,0.00298957,0.546419,0.000155095,0.00118791,0.724441,0.364029,6.58648e-05,0.0148865,0.236293,0.00376371,0.113749,0.379433,0.502911,0.289349,0.0130557,0.889628,0.634568,0.413633,0.0603278,2.83617e-07,0.00482103,0.00319959,0.576935,0.645528,0.159635,0.66902,0.0429004,0.0022837,2.46515e-08,0.000167735,5.53999e-09,0.00493128,0.0579993,0.76203,9.61058e-06,2.24959e-10,0.202633,0.125588,0.00614733,0.00785656,0.00106208,0.385504,0.117909,0.207197,0.019894,0.00906581,0.401684,0.293489,0.130904,0.0157641,0.166956,0.0080909,5.47861e-05,0.733391,0.699838,0.00627586,0.124111,0.573299,0.0018874,0.00565772,0.684354,0.0115219,0.00193984,0.0755187,0.520881,0.000302448,0.0760525,7.9658e-06,5.3813e-07,0.0433986,0.000158317,0.537256,0.00213841,0.804607,0.000147523,0.484879,0.000785993,0.442887,0.111134,0.00165192,0.00100999,0.0177404,0.00681138,0.00222274,0.380263,0.0301143,1.30232e-05,0.573115,0.0358923,0.00190902,0.141644,1.41094e-05,0.117684,0.303513,0.44442,6.86594e-08,0.0108373,0.0242196,0.00458065,0.246113,2.49069e-05,0.126251,0.0157485,0.0202735,0.214535,0.458152,0.0873966,0.109171,0.55014,2.01245e-06,0.180477,0.0504311,0.376936,0.0198305,0.0826206,6.57538e-05,0.463074,0.222529,0.234528,0.00156273,0.00815139,0.0399426,0.001313,0.0251648,0.00570532,0.409798,0.436622,0.143959,0.489702,0.672033,0.0185081,0.480957,0.445913,0.106179,0.296003,0.447485,0.0845698,0.0024453,0.297555,0.410714,0.0324784,0.581581,0.212206,0.31257,0.463718,0.0075811,0.145642,0.169631,0.00384308,0.56248,0.273878,0.0669746,0.154067,0.376098,0.0333383,0.0880462,0.0993883,0.1667,0.133211,0.116907,0.203708,0.0033659,0.00653318,0.361689,0.289284,0.241971,0.00380822,0.151053,0.477267,0.368791,0.00478219,0.00296323,0.297904,0.0476561,0.625257,0.412086,0.371597,0.547611,0.00997787,0.139544,0.04936,0.000251553,0.42109,0.18144,0.00139247,0.0487602,0.455388,0.135754,0.462252,0.0637071,0.435559,0.53418,0.00463579,0.492484,0.529209,0.397471,0.120747,0.330704,0.443138,0.0383448,0.364755,0.312488,0.00135112,0.146184,0.395736,0.404755,0.238065,0.452384,0.0786657,0.0595249,0.481224,0.204547,0.122542,0.259924,0.136638,0.137048,0.00107341,0.194753,0.104944,0.136955,0.085547,0.194507,0.0265104,0.425619,0.50814,0.429061,0.202353,0.240717,0.0139015,0.292976,0.161384,0.255196,0.167238,0.190639,0.307532,0.265287,0.113346,0.168727,0.221472,0.095012,0.320667,0.456504,0.000419456,0.5938,0.107068,0.334729,0.196377,0.0457712,0.448658,0.00542756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}}
}}

Revision as of 12:36, 5 September 2012


Full id: C1091_Neutrophils_Mesenchymal_Monocytederived_Smooth_Hepatic_Prostate_leiomyoma



Phase1 CAGE Peaks

Hg19::chr7:143078652..143078754,+p2@ZYX
Hg19::chr7:143079397..143079426,+p6@ZYX
Hg19::chr7:143079458..143079487,+p4@ZYX
Hg19::chr7:143079496..143079519,+p7@ZYX
Hg19::chr7:143079687..143079742,+p8@ZYX
Hg19::chr7:143079960..143079978,+p3@ZYX
Hg19::chr7:143085915..143085937,+p@chr7:143085915..143085937
+
Hg19::chr7:143085953..143085988,+p@chr7:143085953..143085988
+


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
somatic cell2.75e-26591
mesodermal cell1.07e-18119
multi fate stem cell4.73e-17430
somatic stem cell1.23e-16436
stem cell5.37e-16444
animal cell3.18e-15679
eukaryotic cell3.18e-15679
non-terminally differentiated cell3.77e-15180
contractile cell1.02e-1259
CD14-positive, CD16-negative classical monocyte7.73e-1242
muscle precursor cell2.76e-1157
myoblast2.76e-1157
multi-potent skeletal muscle stem cell2.76e-1157
muscle cell4.26e-1154
smooth muscle cell5.81e-1142
smooth muscle myoblast5.81e-1142
classical monocyte1.04e-1045
myeloid leukocyte1.49e-1076
electrically responsive cell1.78e-1060
electrically active cell1.78e-1060
native cell2.85e-10722
fibroblast3.78e-1075
monopoietic cell4.28e-1063
monocyte4.28e-1063
monoblast4.28e-1063
promonocyte4.28e-1063
embryonic cell5.04e-10248
macrophage dendritic cell progenitor1.76e-0965
vascular associated smooth muscle cell7.25e-0932
lining cell8.12e-0957
barrier cell8.12e-0957
granulocyte monocyte progenitor cell9.82e-0971
myeloid lineage restricted progenitor cell1.48e-0870
connective tissue cell2.52e-08365
endothelial cell2.96e-0835
meso-epithelial cell2.65e-0744
mesenchymal cell3.39e-07358
Uber Anatomy
Ontology termp-valuen
lateral plate mesoderm6.56e-22216
musculoskeletal system2.26e-19167
mesoderm6.97e-19448
mesoderm-derived structure6.97e-19448
presumptive mesoderm6.97e-19448
vasculature5.81e-1679
vascular system5.81e-1679
vessel1.19e-1469
cardiovascular system1.30e-14110
blood vessel3.19e-1460
epithelial tube open at both ends3.19e-1460
blood vasculature3.19e-1460
vascular cord3.19e-1460
somite5.28e-1483
paraxial mesoderm5.28e-1483
presomitic mesoderm5.28e-1483
presumptive segmental plate5.28e-1483
trunk paraxial mesoderm5.28e-1483
presumptive paraxial mesoderm5.28e-1483
circulatory system9.58e-14113
artery1.95e-1342
arterial blood vessel1.95e-1342
arterial system1.95e-1342
splanchnic layer of lateral plate mesoderm3.37e-1384
dermomyotome4.86e-1370
multilaminar epithelium5.95e-1382
trunk mesenchyme1.64e-12143
multi-cellular organism6.70e-11659
muscle tissue1.34e-1063
musculature1.34e-1063
musculature of body1.34e-1063
skeletal muscle tissue1.36e-1061
striated muscle tissue1.36e-1061
myotome1.36e-1061
systemic artery5.23e-1033
systemic arterial system5.23e-1033
anatomical system1.80e-09625
epithelial tube1.90e-09118
anatomical group3.31e-09626
bone marrow1.44e-0880
skeletal element1.58e-08101
skeletal system1.58e-08101
unilaminar epithelium4.52e-08138
hemolymphoid system1.85e-07112
embryo1.88e-07612
connective tissue2.02e-07375
embryonic structure2.18e-07605
developing anatomical structure2.18e-07605
bone element2.21e-0786
germ layer2.57e-07604
embryonic tissue2.57e-07604
presumptive structure2.57e-07604
epiblast (generic)2.57e-07604
trunk7.93e-07216


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)

{{{tfbs_overrepresentation_jaspar}}}



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
EGR1#195853.117611934256340.01051390990388360.0389245741386635



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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