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Coexpression cluster:C1999: Difference between revisions

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{{Coexpression_clusters
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5033,0.44943,0.549618,0.802434,0.25115,0.642741,3.0028,1.90917,2.48134,1.00172,2.53869,0.27659,1.0713,1.1597,0.413782,0.654459,0.388123,0.301779,0.415749,0.580638,1.33238,4.03923,0.824538,1.32072,0.734485,0.609718,0.393318,0.458489,1.91222,0.746838,0.560115,1.08035,1.2359,0.724351,0.4631,0.689906,1.22844,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.741483,0.255232,1.25519,0.917983,2.26106,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.536557,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.367039,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,1.7889,2.31282,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,0.596731,0.897476,2.59175,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,1.41294,0.363423,0.177807,0.126633,1.15522,0.312599,0.736459,1.56426,0.827475,0.439798,1.35505,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.720819|tfbs_overrepresentation_jaspar=MA0003.1;0.481059,MA0004.1;0.626788,MA0006.1;1.14863,MA0007.1;0.606704,MA0009.1;1.11255,MA0014.1;0.369468,MA0017.1;0.496101,MA0019.1;0.784036,MA0024.1;2.29497,MA0025.1;1.24931,MA0027.1;2.73598,MA0028.1;0.470679,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;0.195817,MA0050.1;0.613347,MA0051.1;0.731787,MA0052.1;1.03442,MA0055.1;0.288856,MA0056.1;0,MA0057.1;0.554727,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;5.72676,MA0070.1;1.08584,MA0071.1;0.695094,MA0072.1;1.0812,MA0073.1;0.00220137,MA0074.1;0.730989,MA0076.1;0.540943,MA0077.1;1.07324,MA0078.1;0.836493,MA0081.1;0.522409,MA0083.1;1.12028,MA0084.1;1.62584,MA0087.1;1.07867,MA0088.1;1.3271,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;0.459973,MA0103.1;0.442769,MA0105.1;0.520776,MA0106.1;0.779931,MA0107.1;0.378225,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;0.504689,MA0122.1;1.17777,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;5.12727,MA0146.1;0.0359558,MA0147.1;0.386018,MA0148.1;0.653474,MA0149.1;2.7505,MA0062.2;0.284987,MA0035.2;0.691506,MA0039.2;0.0118463,MA0138.2;0.837782,MA0002.2;0.30855,MA0137.2;0.47779,MA0104.2;0.320919,MA0047.2;0.767096,MA0112.2;0.425004,MA0065.2;0.146576,MA0150.1;0.550239,MA0151.1;0,MA0152.1;0.69926,MA0153.1;1.21379,MA0154.1;0.98952,MA0155.1;0.813062,MA0156.1;1.20729,MA0157.1;0.883854,MA0158.1;0,MA0159.1;0.386729,MA0160.1;0.669748,MA0161.1;0,MA0162.1;0.0592265,MA0163.1;0.168633,MA0164.1;0.810347,MA0080.2;0.456437,MA0018.2;0.781393,MA0099.2;0.699641,MA0079.2;0.00732454,MA0102.2;1.66336,MA0258.1;0.345771,MA0259.1;0.395396,MA0442.1;0}}
|full_id=C1999_Neutrophils_Alveolar_Olfactory_Smooth_Monocytederived_Renal_Dendritic
|id=C1999
}}

Latest revision as of 11:56, 17 September 2013


Full id: C1999_Neutrophils_Alveolar_Olfactory_Smooth_Monocytederived_Renal_Dendritic



Phase1 CAGE Peaks

Hg19::chr7:5567947..5567983,-p10@ACTB
Hg19::chr7:5567987..5568010,-p7@ACTB
Hg19::chr7:5568016..5568065,-p3@ACTB
Hg19::chr7:5568084..5568101,-p14@ACTB
Hg19::chr7:5568284..5568346,-p4@ACTB


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 cell9.55e-22588
animal cell2.67e-18679
eukaryotic cell2.67e-18679
native cell5.91e-13722
mesodermal cell3.70e-11121
somatic stem cell1.07e-10433
multi fate stem cell2.00e-10427
stem cell8.84e-10441
smooth muscle cell7.74e-0943
smooth muscle myoblast7.74e-0943
electrically responsive cell8.24e-0961
electrically active cell8.24e-0961
embryonic cell1.31e-08250
contractile cell3.54e-0859
defensive cell9.31e-0848
phagocyte9.31e-0848
myeloid leukocyte1.04e-0772
muscle precursor cell1.28e-0758
myoblast1.28e-0758
multi-potent skeletal muscle stem cell1.28e-0758
muscle cell1.61e-0755
vascular associated smooth muscle cell2.18e-0732
macrophage dendritic cell progenitor2.75e-0761
monopoietic cell3.24e-0759
monocyte3.24e-0759
monoblast3.24e-0759
promonocyte3.24e-0759
non-terminally differentiated cell6.67e-07106
Uber Anatomy
Ontology termp-valuen
mesoderm2.06e-11315
mesoderm-derived structure2.06e-11315
presumptive mesoderm2.06e-11315
lateral plate mesoderm1.15e-10203
musculoskeletal system6.29e-10167
epithelial vesicle1.35e-0978
vasculature1.02e-0878
vascular system1.02e-0878
multilaminar epithelium1.53e-0783
somite3.31e-0771
presomitic mesoderm3.31e-0771
presumptive segmental plate3.31e-0771
dermomyotome3.31e-0771
trunk paraxial mesoderm3.31e-0771
artery3.40e-0742
arterial blood vessel3.40e-0742
arterial system3.40e-0742
vessel3.53e-0768
cardiovascular system4.20e-07109
dense mesenchyme tissue4.35e-0773
paraxial mesoderm6.98e-0772
presumptive paraxial mesoderm6.98e-0772
muscle tissue7.19e-0764
musculature7.19e-0764
musculature of body7.19e-0764


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)
MA0003.10.481059
MA0004.10.626788
MA0006.11.14863
MA0007.10.606704
MA0009.11.11255
MA0014.10.369468
MA0017.10.496101
MA0019.10.784036
MA0024.12.29497
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
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
MA0048.10.195817
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.10.288856
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.10.321781
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.15.72676
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.10.00220137
MA0074.10.730989
MA0076.10.540943
MA0077.11.07324
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.11.3271
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.10.750974
MA0101.10.459973
MA0103.10.442769
MA0105.10.520776
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
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
MA0145.15.12727
MA0146.10.0359558
MA0147.10.386018
MA0148.10.653474
MA0149.12.7505
MA0062.20.284987
MA0035.20.691506
MA0039.20.0118463
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.425004
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.10.98952
MA0155.10.813062
MA0156.11.20729
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.0592265
MA0163.10.168633
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.20.699641
MA0079.20.00732454
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
BCLAF1#9774521.65264761012182.09874458450681e-071.12118048931615e-05
CTCF#1066444.288205098460020.005152015588243280.0239462107708295
EBF1#187958.9064668465691.78355672307702e-050.000406798166851804
ETS1#211359.728760922202341.14685159850452e-050.000292421958242709
HEY1#2346254.040111043105710.0009288852205177990.00675052839368579
JUND#372756.994663941871035.97069468343598e-050.000985575125720515
MYC#460955.22228187160940.0002573944848850610.00276791830796034
POU2F2#545247.284899246194020.0006631223288743860.00542757311170157
SIN3A#2594244.327107781452110.004977052855762880.0232509582753184
SP1#666755.69838137814090.000166391843712550.00204565011954032
TAF7#6879511.43306940492395.11611886715123e-060.000157570727916959
ZBTB33#10009531.66472502998123.13617771034015e-082.11588671763705e-06



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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