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Coexpression cluster:C1648: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;2.72292,MA0004.1;0.626788,MA0006.1;0.452993,MA0007.1;1.47524,MA0009.1;1.11255,MA0014.1;1.02528,MA0017.1;1.24112,MA0019.1;0.784036,MA0024.1;1.00439,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;2.0635,MA0029.1;1.02437,MA0030.1;1.01252,MA0031.1;0.945567,MA0038.1;0.736268,MA0040.1;1.03042,MA0041.1;0.64667,MA0042.1;0.612397,MA0043.1;1.11288,MA0046.1;1.10134,MA0048.1;1.7027,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;1.01397,MA0056.1;0,MA0057.1;0.189508,MA0058.1;0.523638,MA0059.1;0.522232,MA0060.1;0.321781,MA0061.1;0.291022,MA0063.1;0,MA0066.1;0.736721,MA0067.1;1.43651,MA0068.1;0.247962,MA0069.1;1.09737,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;2.08296,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;2.43492,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;0.132006,MA0089.1;0,MA0090.1;0.556637,MA0091.1;0.629594,MA0092.1;0.588959,MA0093.1;0.456342,MA0095.1;0,MA0098.1;0,MA0100.1;0.750974,MA0101.1;3.01022,MA0103.1;0.442769,MA0105.1;0.175503,MA0106.1;0.779931,MA0107.1;1.74965,MA0108.2;0.94238,MA0109.1;0,MA0111.1;0.5713,MA0113.1;0.797251,MA0114.1;0.372523,MA0115.1;1.35895,MA0116.1;0.382106,MA0117.1;1.1512,MA0119.1;1.25946,MA0122.1;4.2893,MA0124.1;1.31673,MA0125.1;1.23103,MA0130.1;0,MA0131.1;0.855546,MA0132.1;0,MA0133.1;0,MA0135.1;1.14377,MA0136.1;0.743749,MA0139.1;0.277033,MA0140.1;0.692258,MA0141.1;0.520334,MA0142.1;0.912455,MA0143.1;0.797437,MA0144.1;0.356507,MA0145.1;0.442008,MA0146.1;1.82062,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;0.681935,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.15493,MA0138.2;0.837782,MA0002.2;0.83106,MA0137.2;0.47779,MA0104.2;1.54865,MA0047.2;0.767096,MA0112.2;1.96224,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.172764,MA0155.1;1.91168,MA0156.1;0.480289,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.21472,MA0163.1;0.0439995,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.0198381,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0
}}
}}

Revision as of 20:05, 22 January 2013


Full id: C1648_Adipocyte_Ciliary_Endothelial_Smooth_aorta_kidney_hepatic



Phase1 CAGE Peaks

Hg19::chr11:89224488..89224507,-p3@NOX4
Hg19::chr11:89224508..89224563,-p1@NOX4
Hg19::chr11:89224580..89224594,-p4@NOX4
Hg19::chr11:89224638..89224649,-p6@NOX4
Hg19::chr11:89224667..89224681,-p2@NOX4


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
endothelial cell of vascular tree4.77e-2224
blood vessel endothelial cell1.06e-1718
embryonic blood vessel endothelial progenitor cell1.06e-1718
mesodermal cell2.56e-15121
endothelial cell2.70e-1536
vascular associated smooth muscle cell1.20e-1232
non-terminally differentiated cell2.53e-12106
meso-epithelial cell3.43e-1145
electrically responsive cell3.91e-1161
electrically active cell3.91e-1161
muscle precursor cell8.45e-1058
myoblast8.45e-1058
multi-potent skeletal muscle stem cell8.45e-1058
contractile cell1.15e-0959
muscle cell1.34e-0955
endothelial cell of artery2.10e-099
smooth muscle cell3.16e-0943
smooth muscle myoblast3.16e-0943
embryonic cell1.03e-08250
aortic smooth muscle cell1.70e-0710
vein endothelial cell3.04e-076
lining cell3.77e-0758
barrier cell3.77e-0758
aortic endothelial cell4.67e-076
Uber Anatomy
Ontology termp-valuen
vasculature4.98e-3578
vascular system4.98e-3578
vessel7.44e-3268
epithelial tube open at both ends6.92e-3059
blood vessel6.92e-3059
blood vasculature6.92e-3059
vascular cord6.92e-3059
splanchnic layer of lateral plate mesoderm1.30e-2783
circulatory system2.47e-27112
cardiovascular system6.14e-27109
epithelial tube3.13e-21117
artery1.76e-2042
arterial blood vessel1.76e-2042
arterial system1.76e-2042
blood vessel endothelium1.06e-1718
endothelium1.06e-1718
cardiovascular system endothelium1.06e-1718
systemic artery1.91e-1533
systemic arterial system1.91e-1533
simple squamous epithelium4.23e-1322
cell layer6.37e-13309
tube1.23e-12192
anatomical cluster2.70e-12373
aorta3.93e-1221
aortic system3.93e-1221
epithelium6.25e-12306
unilaminar epithelium2.61e-11148
skeletal muscle tissue5.57e-1162
striated muscle tissue5.57e-1162
myotome5.57e-1162
muscle tissue6.00e-1164
musculature6.00e-1164
musculature of body6.00e-1164
epithelial vesicle6.06e-1178
anatomical conduit1.12e-10240
squamous epithelium1.14e-1025
paraxial mesoderm1.20e-0972
presumptive paraxial mesoderm1.20e-0972
endothelial tube2.10e-099
arterial system endothelium2.10e-099
endothelium of artery2.10e-099
somite2.23e-0971
presomitic mesoderm2.23e-0971
presumptive segmental plate2.23e-0971
dermomyotome2.23e-0971
trunk paraxial mesoderm2.23e-0971
dense mesenchyme tissue2.40e-0973
multi-cellular organism2.74e-09656
pigment epithelium of eye8.04e-0911
vein5.07e-089
venous blood vessel5.07e-089
venous system5.07e-089
umbilical blood vessel7.57e-089
blood vessel smooth muscle1.70e-0710
arterial system smooth muscle1.70e-0710
artery smooth muscle tissue1.70e-0710
aorta smooth muscle tissue1.70e-0710
multilaminar epithelium1.74e-0783
omentum5.06e-076
peritoneum5.06e-076
abdominal cavity5.06e-076
visceral peritoneum5.06e-076
mesoderm9.75e-07315
mesoderm-derived structure9.75e-07315
presumptive mesoderm9.75e-07315


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)
MA0003.12.72292
MA0004.10.626788
MA0006.10.452993
MA0007.11.47524
MA0009.11.11255
MA0014.11.02528
MA0017.11.24112
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.12.0635
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.7027
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.11.01397
MA0056.10
MA0057.10.189508
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.12.08296
MA0074.10.730989
MA0076.10.540943
MA0077.12.43492
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.13.01022
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.11.74965
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.11.25946
MA0122.14.2893
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.277033
MA0140.10.692258
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.11.82062
MA0147.10.386018
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.15493
MA0138.20.837782
MA0002.20.83106
MA0137.20.47779
MA0104.21.54865
MA0047.20.767096
MA0112.21.96224
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.172764
MA0155.11.91168
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.21472
MA0163.10.0439995
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.0198381
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
JUND#372756.994663941871035.97069468343598e-050.000983089046261028
SP1#666755.69838137814090.000166391843712550.00204036606381296
TAF1#687253.343046285745290.002394600090870310.0135168975727167
TAF7#6879511.43306940492395.11611886715123e-060.000157246126652857
TBP#690853.706770687096390.001428755106721120.0091775481020264
YY1#752843.928936599883080.007193866269917620.0298332353622906



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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