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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:36, 17 September 2013


Full id: C1050_brain_diencephalon_substantia_corpus_occipital_optic_spinal



Phase1 CAGE Peaks

Hg19::chr17:40123919..40123952,+p6@CNP
Hg19::chr17:56598639..56598652,-p@chr17:56598639..56598652
-
Hg19::chr19:36362881..36362902,+p@chr19:36362881..36362902
+
Hg19::chr19:36367441..36367488,+p@chr19:36367441..36367488
+
Hg19::chr19:36370032..36370046,+p@chr19:36370032..36370046
+
Hg19::chr2:128403581..128403584,+p6@GPR17
Hg19::chr2:233740296..233740309,+p10@C2orf82
Hg19::chr2:96686244..96686248,+p@chr2:96686244..96686248
+


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:00041132',3'-cyclic-nucleotide 3'-phosphodiesterase activity0.0041209802018991
GO:0009214cyclic nucleotide catabolic process0.0041209802018991
GO:0009166nucleotide catabolic process0.017158619785766
GO:0001637G-protein chemoattractant receptor activity0.017158619785766
GO:0004950chemokine receptor activity0.017158619785766
GO:0019956chemokine binding0.017158619785766
GO:0001608nucleotide receptor activity, G-protein coupled0.017158619785766
GO:0045028purinergic nucleotide receptor activity, G-protein coupled0.017158619785766
GO:0016502nucleotide receptor activity0.017158619785766
GO:0001614purinergic nucleotide receptor activity0.017158619785766
GO:0004112cyclic-nucleotide phosphodiesterase activity0.017158619785766
GO:0009187cyclic nucleotide metabolic process0.017158619785766
GO:0048770pigment granule0.0244023979519757
GO:0042470melanosome0.0244023979519757
GO:0019955cytokine binding0.027159637823942
GO:0008081phosphoric diester hydrolase activity0.0338108017026104
GO:0001653peptide receptor activity0.0338108017026104
GO:0008528peptide receptor activity, G-protein coupled0.0338108017026104
GO:0042277peptide binding0.0449771012983651



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
neuronal stem cell9.60e-108
neuron2.71e-096
neuroblast2.71e-096
electrically signaling cell2.71e-096
Uber Anatomy
Ontology termp-valuen
neural tube3.19e-7756
neural rod3.19e-7756
future spinal cord3.19e-7756
neural keel3.19e-7756
central nervous system8.75e-7481
nervous system8.88e-7189
regional part of nervous system3.52e-7053
regional part of brain3.52e-7053
brain1.89e-5768
future brain1.89e-5768
regional part of forebrain9.22e-5541
forebrain9.22e-5541
anterior neural tube9.22e-5541
future forebrain9.22e-5541
neural plate4.26e-5482
presumptive neural plate4.26e-5482
neurectoderm2.23e-5386
brain grey matter1.60e-5034
gray matter1.60e-5034
telencephalon2.07e-5034
regional part of telencephalon6.47e-4632
cerebral hemisphere1.39e-4532
adult organism1.99e-43114
ecto-epithelium6.57e-42104
pre-chordal neural plate7.11e-3961
structure with developmental contribution from neural crest5.43e-35132
ectoderm-derived structure1.88e-34171
ectoderm1.88e-34171
presumptive ectoderm1.88e-34171
regional part of cerebral cortex1.14e-3122
cerebral cortex1.53e-3025
pallium1.53e-3025
neocortex2.43e-2720
organ system subdivision6.01e-24223
neural nucleus1.31e-229
nucleus of brain1.31e-229
posterior neural tube1.43e-2215
chordal neural plate1.43e-2215
tube1.49e-18192
segmental subdivision of nervous system3.71e-1813
telencephalic nucleus6.95e-187
basal ganglion1.12e-179
nuclear complex of neuraxis1.12e-179
aggregate regional part of brain1.12e-179
collection of basal ganglia1.12e-179
cerebral subcortex1.12e-179
segmental subdivision of hindbrain6.05e-1612
hindbrain6.05e-1612
presumptive hindbrain6.05e-1612
brainstem1.76e-156
anatomical cluster2.19e-13373
anatomical conduit4.91e-13240
occipital lobe6.79e-135
epithelium3.22e-11306
cell layer5.62e-11309
corpus striatum1.61e-104
striatum1.61e-104
ventral part of telencephalon1.61e-104
future corpus striatum1.61e-104
gyrus1.71e-106
regional part of metencephalon9.26e-109
metencephalon9.26e-109
future metencephalon9.26e-109
organ part1.08e-09218
spinal cord9.14e-093
dorsal region element9.14e-093
dorsum9.14e-093
pons1.34e-083
medulla oblongata1.44e-083
myelencephalon1.44e-083
future myelencephalon1.44e-083
caudate-putamen1.94e-083
dorsal striatum1.94e-083
limbic system2.00e-085
parietal lobe2.20e-085
multi-tissue structure7.39e-08342


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)
MA0003.10.140538
MA0004.10.455723
MA0006.10.300178
MA0007.11.1148
MA0009.10.918715
MA0014.10.134069
MA0017.10.896777
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.315574
MA0029.10.832916
MA0030.10.821423
MA0031.10.756713
MA0038.10.557409
MA0040.10.838784
MA0041.10.474018
MA0042.10.442535
MA0043.10.919032
MA0046.10.90778
MA0048.10.316923
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.11.2107
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.497495
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.10.415214
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.634172
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.361233
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.11.17773
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.792149
MA0105.10.279181
MA0106.10.59853
MA0107.10.666147
MA0108.20.753643
MA0109.10
MA0111.11.04489
MA0113.10.614917
MA0114.11.22129
MA0115.11.1606
MA0116.11.25157
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.11.17059
MA0145.10.830366
MA0146.11.63914
MA0147.10.243042
MA0148.10.480298
MA0149.10.506665
MA0062.20.161302
MA0035.20.515566
MA0039.20.164269
MA0138.20.653421
MA0002.20.179788
MA0137.20.86081
MA0104.20.189646
MA0047.20.586412
MA0112.20.208783
MA0065.21.27835
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.12.00298
MA0155.10.43752
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.11.26616
MA0160.10.495355
MA0161.10
MA0162.10.0163939
MA0163.11.06699
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.13841
MA0102.21.46209
MA0258.10.209744
MA0259.10.25092
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.