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Coexpression cluster:C2611: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.590005,1.54039,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.462021,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.505745,0.731221,0.528529,0.632849,0.892087,0.849366,0.728867,0.537869,0.297585,0.682839,1.09415,0.433165,1.63198,0.49475,0.285913,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.648765,0.61613,0.822818,0.694903,0.173425,1.33034,0.90714,0.83543,0.699149,1.17354,1.33024,0.812467,0.54284,0.777235,1.46445,0.776148,1.13655,0.825354,1.0193,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,1.5667,0.402607,0.692875,1.32819,0.893276,0.321165,0.823598,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,1.17995,0.221873,0.793068,0.934646,1.89266,1.51507,1.24792,1.11156,1.966,0.535192,0.456994,0.934671,1.15558,0.939507,0.749003,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,0.681522,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,1.15964,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.66252,0.521611,1.24902,0.997363,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,1.00378
|tfbs_overrepresentation_jaspar=MA0003.1;1.45381,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.524262,MA0017.1;0.577281,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;1.98521,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.841508,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.866596,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;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;2.29123,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;2.01886,MA0107.1;2.00595,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,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;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;0.430413,MA0145.1;0.195821,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;1.813,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;2.01147,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;1.05083,MA0065.2;1.7213,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;1.21162,MA0155.1;2.30186,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.640035,MA0163.1;1.90765,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;1.38179,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:47, 22 January 2013


Full id: C2611_Hepatic_heart_breast_Renal_spleen_Endothelial_acute



Phase1 CAGE Peaks

Hg19::chr20:30598204..30598223,+p3@C20orf160
Hg19::chr20:30598231..30598260,+p2@C20orf160
Hg19::chr22:51111241..51111260,+p@chr22:51111241..51111260
+
Hg19::chr3:123751833..123751848,+p@chr3:123751833..123751848
+


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
adult organism2.22e-72114
neural tube7.62e-2756
neural rod7.62e-2756
future spinal cord7.62e-2756
neural keel7.62e-2756
anatomical conduit1.04e-26240
anatomical cluster6.16e-26373
regional part of nervous system1.03e-2453
regional part of brain1.03e-2453
tube2.71e-23192
regional part of forebrain6.19e-2241
forebrain6.19e-2241
anterior neural tube6.19e-2241
future forebrain6.19e-2241
neural plate8.33e-2182
presumptive neural plate8.33e-2182
blood vessel endothelium1.33e-2018
endothelium1.33e-2018
cardiovascular system endothelium1.33e-2018
central nervous system7.99e-2081
brain2.53e-1968
future brain2.53e-1968
neurectoderm3.97e-1986
brain grey matter1.78e-1734
gray matter1.78e-1734
nervous system2.38e-1789
telencephalon3.21e-1734
regional part of telencephalon5.35e-1632
cerebral hemisphere5.79e-1632
simple squamous epithelium1.06e-1522
structure with developmental contribution from neural crest2.91e-15132
pre-chordal neural plate2.00e-1461
ecto-epithelium3.69e-14104
regional part of cerebral cortex4.05e-1422
organ system subdivision3.73e-13223
squamous epithelium4.36e-1325
neocortex1.27e-1220
epithelium6.56e-12306
cerebral cortex8.15e-1225
pallium8.15e-1225
cell layer1.51e-11309
vessel2.84e-1168
multi-cellular organism4.78e-11656
endothelial tube8.66e-119
arterial system endothelium8.66e-119
endothelium of artery8.66e-119
anatomical system1.88e-09624
anatomical group2.26e-09625
multi-tissue structure3.42e-09342
vasculature3.47e-0978
vascular system3.47e-0978
lymphoid system5.90e-0910
splanchnic layer of lateral plate mesoderm3.15e-0883
ectoderm-derived structure4.33e-08171
ectoderm4.33e-08171
presumptive ectoderm4.33e-08171
circulatory system5.63e-08112
organ part6.18e-08218
embryo1.21e-07592
epithelial tube open at both ends1.38e-0759
blood vessel1.38e-0759
blood vasculature1.38e-0759
vascular cord1.38e-0759
lymphatic vessel1.96e-078
lymph vasculature1.96e-078
lymphatic part of lymphoid system1.96e-078
neural nucleus2.43e-079
nucleus of brain2.43e-079
embryonic structure4.17e-07564
germ layer5.44e-07560
germ layer / neural crest5.44e-07560
embryonic tissue5.44e-07560
presumptive structure5.44e-07560
germ layer / neural crest derived structure5.44e-07560
epiblast (generic)5.44e-07560
developing anatomical structure5.69e-07581
compound organ7.75e-0768


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)
MA0003.11.45381
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.524262
MA0017.10.577281
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
MA0057.11.98521
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.841508
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.866596
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
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.12.29123
MA0103.10.521546
MA0105.10.232357
MA0106.12.01886
MA0107.12.00595
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
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
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.11.813
MA0062.20.353589
MA0035.20.778873
MA0039.22.01147
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.21.05083
MA0065.21.7213
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.11.21162
MA0155.12.30186
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.640035
MA0163.11.90765
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
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

No analysis results for this cluster

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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