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Coexpression cluster:C2346: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.443649,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.244769,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;1.30988,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.791759,MA0056.1;0,MA0057.1;1.28333,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;0.393285,MA0061.1;0.946082,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;2.83685,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;1.32557,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;1.1497,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;0.481,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;0.769072,MA0062.2;0.931615,MA0035.2;0.778873,MA0039.2;0.483275,MA0138.2;0.928035,MA0002.2;0.379056,MA0137.2;0.558189,MA0104.2;1.01696,MA0047.2;0.856092,MA0112.2;0.551048,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;1.02191,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;1.1691,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.309472,MA0163.1;0.253219,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;1.1888,MA0442.1;0
}}
}}

Revision as of 20:35, 22 January 2013


Full id: C2346_optic_testis_brain_medulla_spinal_duodenum_caudate



Phase1 CAGE Peaks

Hg19::chr15:69278159..69278160,+p@chr15:69278159..69278160
+
Hg19::chr18:74692220..74692236,+p@chr18:74692220..74692236
+
Hg19::chr6:52268150..52268166,+p6@PAQR8
Hg19::chr8:22411901..22411915,+p45@SORBS3


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:0051496positive regulation of stress fiber formation0.00553339899145803
GO:0051495positive regulation of cytoskeleton organization and biogenesis0.00553339899145803
GO:0032233positive regulation of actin filament bundle formation0.00553339899145803
GO:0017166vinculin binding0.00553339899145803
GO:0032231regulation of actin filament bundle formation0.00553339899145803
GO:0051492regulation of stress fiber formation0.00553339899145803
GO:0043149stress fiber formation0.00553339899145803
GO:0043410positive regulation of MAPKKK cascade0.00553339899145803
GO:0051130positive regulation of cellular component organization and biogenesis0.00829924324777567
GO:0043408regulation of MAPKKK cascade0.00829924324777567
GO:0051017actin filament bundle formation0.00955614159098618
GO:0005925focal adhesion0.0151172769961849
GO:0005924cell-substrate adherens junction0.0151172769961849
GO:0030055cell-matrix junction0.0151172769961849
GO:0007015actin filament organization0.0151172769961849
GO:0005912adherens junction0.0172028556795746
GO:0051493regulation of cytoskeleton organization and biogenesis0.0172028556795746
GO:0033043regulation of organelle organization and biogenesis0.0172028556795746
GO:0005200structural constituent of cytoskeleton0.0223717054781359
GO:0005496steroid binding0.0223717054781359
GO:0016323basolateral plasma membrane0.0223717054781359
GO:0051128regulation of cellular component organization and biogenesis0.0247453519321812
GO:0031589cell-substrate adhesion0.0247453519321812
GO:0000122negative regulation of transcription from RNA polymerase II promoter0.0292296123884345
GO:0000165MAPKKK cascade0.0324924248843825
GO:0009967positive regulation of signal transduction0.0324924248843825
GO:0045892negative regulation of transcription, DNA-dependent0.0414835460253769
GO:0005886plasma membrane0.0423490121090567
GO:0030036actin cytoskeleton organization and biogenesis0.0469634907591985
GO:0030029actin filament-based process0.0477782347950747



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
neural tube2.05e-6756
neural rod2.05e-6756
future spinal cord2.05e-6756
neural keel2.05e-6756
regional part of nervous system2.14e-6353
regional part of brain2.14e-6353
central nervous system5.32e-5781
nervous system3.44e-5389
regional part of forebrain7.75e-5341
forebrain7.75e-5341
anterior neural tube7.75e-5341
future forebrain7.75e-5341
brain8.03e-5368
future brain8.03e-5368
brain grey matter1.37e-5134
gray matter1.37e-5134
telencephalon2.17e-5134
neural plate2.22e-4882
presumptive neural plate2.22e-4882
neurectoderm3.92e-4886
regional part of telencephalon2.90e-4632
cerebral hemisphere5.47e-4632
adult organism1.78e-40114
ecto-epithelium4.92e-38104
pre-chordal neural plate5.93e-3661
regional part of cerebral cortex2.25e-2922
cerebral cortex8.74e-2925
pallium8.74e-2925
neocortex2.37e-2820
ectoderm-derived structure4.34e-28171
ectoderm4.34e-28171
presumptive ectoderm4.34e-28171
structure with developmental contribution from neural crest9.80e-28132
neural nucleus1.06e-269
nucleus of brain1.06e-269
telencephalic nucleus4.99e-217
basal ganglion6.37e-219
nuclear complex of neuraxis6.37e-219
aggregate regional part of brain6.37e-219
collection of basal ganglia6.37e-219
cerebral subcortex6.37e-219
organ system subdivision8.49e-21223
tube7.56e-19192
brainstem3.45e-186
posterior neural tube3.34e-1515
chordal neural plate3.34e-1515
anatomical conduit1.03e-14240
segmental subdivision of nervous system5.20e-1413
gyrus1.88e-126
corpus striatum2.81e-124
striatum2.81e-124
ventral part of telencephalon2.81e-124
future corpus striatum2.81e-124
segmental subdivision of hindbrain1.38e-1112
hindbrain1.38e-1112
presumptive hindbrain1.38e-1112
anatomical cluster5.80e-11373
temporal lobe8.11e-116
medulla oblongata5.20e-103
myelencephalon5.20e-103
future myelencephalon5.20e-103
pons6.82e-103
epithelium7.24e-10306
parietal lobe8.97e-105
cell layer1.15e-09309
caudate-putamen1.20e-093
dorsal striatum1.20e-093
organ part4.20e-09218
multi cell component structure1.38e-072
neuron projection bundle1.38e-072
globus pallidus1.67e-072
pallidum1.67e-072
multi-tissue structure1.70e-07342
dorsal plus ventral thalamus1.72e-072
thalamic complex1.72e-072
locus ceruleus2.28e-072
brainstem nucleus2.28e-072
hindbrain nucleus2.28e-072
caudate nucleus5.49e-072
future caudate nucleus5.49e-072
middle temporal gyrus5.66e-072


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
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.244769
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
MA0048.11.30988
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.791759
MA0056.10
MA0057.11.28333
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.946082
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.12.83685
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
MA0093.11.32557
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.11.1497
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
MA0146.10.481
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.931615
MA0035.20.778873
MA0039.20.483275
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.21.01696
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.02191
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.11.1691
MA0160.10.756582
MA0161.10
MA0162.10.309472
MA0163.10.253219
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.21.38179
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

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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2346&oldid=2570857"