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Coexpression cluster:C4175: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;3.8806,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;1.80735,MA0017.1;1.64148,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;3.9895,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.407479,MA0074.1;0.935474,MA0076.1;0.734647,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;0.257905,MA0089.1;0,MA0090.1;0.751469,MA0091.1;0.829044,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.846801,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.707589,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;0.449458,MA0035.2;0.894194,MA0039.2;1.15986,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;0.666381,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.731309,MA0065.2;0.760954,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.312019,MA0155.1;2.83144,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;1.43223,MA0163.1;1.2663,MA0164.1;1.01792,MA0080.2;0.643061,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;4.10519,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;1.40979,MA0442.1;0
}}
}}

Revision as of 21:53, 22 January 2013


Full id: C4175_putamen_pons_heart_occipital_parietal_medial_paracentral



Phase1 CAGE Peaks

Hg19::chr2:207308220..207308267,+p1@ADAM23
Hg19::chr2:207308275..207308295,+p2@ADAM23
Hg19::chr2:207308554..207308568,+p5@ADAM23


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
nervous system2.17e-3189
central nervous system4.05e-3081
cell layer4.79e-29309
epithelium6.29e-29306
neural plate1.83e-2882
presumptive neural plate1.83e-2882
neurectoderm2.30e-2786
neural tube1.82e-2656
neural rod1.82e-2656
future spinal cord1.82e-2656
neural keel1.82e-2656
anatomical cluster1.45e-25373
regional part of nervous system5.50e-2553
regional part of brain5.50e-2553
brain1.03e-2468
future brain1.03e-2468
tube2.19e-23192
structure with developmental contribution from neural crest2.79e-23132
ecto-epithelium3.53e-22104
ectoderm-derived structure1.19e-21171
ectoderm1.19e-21171
presumptive ectoderm1.19e-21171
regional part of forebrain2.06e-2141
forebrain2.06e-2141
anterior neural tube2.06e-2141
future forebrain2.06e-2141
anatomical conduit2.56e-21240
pre-chordal neural plate3.89e-2161
brain grey matter7.12e-1934
gray matter7.12e-1934
telencephalon7.61e-1934
cerebral hemisphere1.88e-1832
regional part of telencephalon8.96e-1832
vasculature2.54e-1678
vascular system2.54e-1678
adult organism3.48e-16114
epithelial tube open at both ends1.34e-1559
blood vessel1.34e-1559
blood vasculature1.34e-1559
vascular cord1.34e-1559
vessel5.86e-1568
multi-tissue structure1.01e-14342
circulatory system1.06e-14112
splanchnic layer of lateral plate mesoderm1.22e-1483
regional part of cerebral cortex1.41e-1422
cerebral cortex1.86e-1425
pallium1.86e-1425
neocortex1.97e-1320
cardiovascular system2.04e-13109
organ system subdivision5.75e-13223
artery8.54e-1342
arterial blood vessel8.54e-1342
arterial system8.54e-1342
multi-cellular organism2.51e-12656
skeletal muscle tissue3.03e-1262
striated muscle tissue3.03e-1262
myotome3.03e-1262
muscle tissue1.16e-1164
musculature1.16e-1164
musculature of body1.16e-1164
dense mesenchyme tissue1.53e-1173
embryo1.71e-11592
paraxial mesoderm2.31e-1172
presumptive paraxial mesoderm2.31e-1172
somite6.64e-1171
presomitic mesoderm6.64e-1171
presumptive segmental plate6.64e-1171
dermomyotome6.64e-1171
trunk paraxial mesoderm6.64e-1171
germ layer9.97e-11560
germ layer / neural crest9.97e-11560
embryonic tissue9.97e-11560
presumptive structure9.97e-11560
germ layer / neural crest derived structure9.97e-11560
epiblast (generic)9.97e-11560
embryonic structure1.19e-10564
anatomical group1.54e-10625
anatomical system2.04e-10624
epithelial vesicle1.14e-0978
systemic artery1.34e-0933
systemic arterial system1.34e-0933
developing anatomical structure3.17e-09581
multilaminar epithelium1.85e-0883
unilaminar epithelium1.45e-07148
organ part2.03e-07218
aorta2.57e-0721
aortic system2.57e-0721


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)
MA0003.13.8806
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.11.80735
MA0017.11.64148
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.13.9895
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.407479
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.846801
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.21.15986
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.12.83144
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.11.43223
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.24.10519
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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
EGR1#195834.988179094810140.008056488137383440.0321370240844928



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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