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Coexpression cluster:C2076: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;0.71247,MA0006.1;2.26728,MA0007.1;1.65296,MA0009.1;1.20602,MA0014.1;1.34758,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;0.709734,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,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;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.100363,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;1.62583,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;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,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;0.912459,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;0.481,MA0147.1;1.16748,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.257871,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.187982,MA0065.2;0.199162,MA0150.1;0.633493,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;0.533581,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;1.06783,MA0163.1;1.37853,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.476674,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;1.1888,MA0442.1;0
}}
}}

Revision as of 20:23, 22 January 2013


Full id: C2076_Melanocyte_corpus_brain_occipital_temporal_postcentral_pons



Phase1 CAGE Peaks

Hg19::chr10:83635613..83635633,+p3@NRG3
Hg19::chr8:22005612..22005623,-p@chr8:22005612..22005623
-
Hg19::chr8:22014298..22014326,-p1@LGI3
Hg19::chr8:22014339..22014342,-p4@LGI3


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

GO IDGO nameFDR corrected p-value
GO:0030297transmembrane receptor protein tyrosine kinase activator activity0.00565129725365418
GO:0030971receptor tyrosine kinase binding0.00565129725365418
GO:0030296protein tyrosine kinase activator activity0.00565129725365418
GO:0030295protein kinase activator activity0.00791088449005495
GO:0030879mammary gland development0.00791088449005495
GO:0019209kinase activator activity0.00847544856163342
GO:0048732gland development0.0185576153148636
GO:0019887protein kinase regulator activity0.0370325943749413
GO:0019207kinase regulator activity0.0382378355329935
GO:0001558regulation of cell growth0.0446438476068774
GO:0016049cell growth0.0446438476068774
GO:0040008regulation of growth0.0446438476068774
GO:0008361regulation of cell size0.0446438476068774
GO:0009790embryonic development0.0472706531134139
GO:0008083growth factor activity0.0474859976685569



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
melanocyte7.62e-1310
melanoblast7.62e-1310
pigment cell9.84e-0914
light melanocyte4.22e-073
Uber Anatomy
Ontology termp-valuen
neural tube1.69e-7856
neural rod1.69e-7856
future spinal cord1.69e-7856
neural keel1.69e-7856
regional part of nervous system2.32e-7253
regional part of brain2.32e-7253
regional part of forebrain4.98e-6341
forebrain4.98e-6341
anterior neural tube4.98e-6341
future forebrain4.98e-6341
adult organism2.05e-62114
central nervous system9.29e-6281
brain5.03e-6168
future brain5.03e-6168
neural plate1.19e-5682
presumptive neural plate1.19e-5682
nervous system1.38e-5689
neurectoderm2.41e-5386
telencephalon2.52e-5334
brain grey matter5.40e-5334
gray matter5.40e-5334
cerebral hemisphere6.92e-4932
regional part of telencephalon7.06e-4932
ecto-epithelium1.27e-45104
pre-chordal neural plate5.02e-4461
regional part of cerebral cortex9.51e-4122
structure with developmental contribution from neural crest3.50e-37132
neocortex6.70e-3720
cerebral cortex2.89e-3525
pallium2.89e-3525
ectoderm-derived structure1.12e-28171
ectoderm1.12e-28171
presumptive ectoderm1.12e-28171
organ system subdivision8.65e-23223
basal ganglion1.74e-199
nuclear complex of neuraxis1.74e-199
aggregate regional part of brain1.74e-199
collection of basal ganglia1.74e-199
cerebral subcortex1.74e-199
neural nucleus2.46e-199
nucleus of brain2.46e-199
tube1.27e-18192
posterior neural tube3.58e-1615
chordal neural plate3.58e-1615
telencephalic nucleus2.85e-157
anatomical conduit4.95e-15240
gyrus1.90e-146
brainstem8.13e-146
segmental subdivision of nervous system1.53e-1213
epithelium1.93e-12306
anatomical cluster2.88e-12373
cell layer3.62e-12309
parietal lobe4.15e-125
occipital lobe5.08e-125
limbic system1.23e-115
segmental subdivision of hindbrain6.65e-1112
hindbrain6.65e-1112
presumptive hindbrain6.65e-1112
diencephalon7.76e-117
future diencephalon7.76e-117
organ part1.39e-10218
multi-tissue structure2.52e-10342
corpus striatum2.15e-094
striatum2.15e-094
ventral part of telencephalon2.15e-094
future corpus striatum2.15e-094
regional part of diencephalon4.38e-094
temporal lobe1.24e-086
frontal cortex7.62e-083
pons8.92e-083
medulla oblongata1.04e-073
myelencephalon1.04e-073
future myelencephalon1.04e-073
spinal cord1.42e-073
dorsal region element1.42e-073
dorsum1.42e-073
caudate-putamen1.94e-073
dorsal striatum1.94e-073
organ2.25e-07503


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)
MA0003.10.443649
MA0004.10.71247
MA0006.12.26728
MA0007.11.65296
MA0009.11.20602
MA0014.11.34758
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
MA0048.10.709734
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
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
MA0139.10.912459
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.10.430413
MA0145.10.195821
MA0146.10.481
MA0147.11.16748
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.257871
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.187982
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.533581
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.11.06783
MA0163.11.37853
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.476674
MA0102.21.75932
MA0258.10.418966
MA0259.11.1888
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
SUZ12#23512225.05789045553150.002325256716520610.0131831869180118



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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