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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:32, 17 September 2013


Full id: C877_optic_parietal_occipital_temporal_corpus_duodenum_brain



Phase1 CAGE Peaks

Hg19::chr11:113075052..113075072,+p@chr11:113075052..113075072
+
Hg19::chr11:117667885..117667949,-p1@DSCAML1
Hg19::chr11:131309852..131309856,+p@chr11:131309852..131309856
+
Hg19::chr11:131433495..131433499,+p@chr11:131433495..131433499
+
Hg19::chr11:66059302..66059313,+p3@TMEM151A
Hg19::chr15:84116080..84116099,+p2@SH3GL3
Hg19::chr1:147718685..147718722,-p@chr1:147718685..147718722
-
Hg19::chr2:27170707..27170718,+p6@DPYSL5
Hg19::chr6:124124993..124125015,+p6@NKAIN2


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:0007399nervous system development0.00235882184034278
GO:0007409axonogenesis0.00235882184034278
GO:0048667neuron morphogenesis during differentiation0.00235882184034278
GO:0048812neurite morphogenesis0.00235882184034278
GO:0000904cellular morphogenesis during differentiation0.00235882184034278
GO:0031175neurite development0.00235882184034278
GO:0048666neuron development0.00263048050948375
GO:0032990cell part morphogenesis0.00310783649624717
GO:0048858cell projection morphogenesis0.00310783649624717
GO:0030030cell projection organization and biogenesis0.00310783649624717
GO:0030182neuron differentiation0.00310783649624717
GO:0007417central nervous system development0.00348781455915125
GO:0048699generation of neurons0.00348781455915125
GO:0022008neurogenesis0.00379284252160859
GO:0048731system development0.00594289024873574
GO:0042802identical protein binding0.00637410169344523
GO:0048704embryonic skeletal morphogenesis0.00708727549592255
GO:0048856anatomical structure development0.00832386365774856
GO:0048706embryonic skeletal development0.00832386365774856
GO:0000902cell morphogenesis0.00832386365774856
GO:0032989cellular structure morphogenesis0.00832386365774856
GO:0048705skeletal morphogenesis0.00912432801082624
GO:0031901early endosome membrane0.00989013586888669
GO:0007275multicellular organismal development0.0105791378658706
GO:0009953dorsal/ventral pattern formation0.014914166630396
GO:0001709cell fate determination0.014914166630396
GO:0043025cell soma0.0173270730176464
GO:0030425dendrite0.018137180821599
GO:0005769early endosome0.0225663353440213
GO:0016043cellular component organization and biogenesis0.0233626455106897
GO:0032502developmental process0.0233626455106897
GO:0007411axon guidance0.0233626455106897
GO:0009653anatomical structure morphogenesis0.0245951547792637
GO:0045165cell fate commitment0.0278535056622883
GO:0043005neuron projection0.0289834837544392
GO:0032501multicellular organismal process0.0289834837544392
GO:0048468cell development0.0289834837544392
GO:0010008endosome membrane0.0289834837544392
GO:0044440endosomal part0.0289834837544392
GO:0003002regionalization0.0289834837544392
GO:0048598embryonic morphogenesis0.0294267243002979
GO:0009792embryonic development ending in birth or egg hatching0.0294267243002979
GO:0043009chordate embryonic development0.0294267243002979
GO:0007389pattern specification process0.037472638517259
GO:0007420brain development0.0410359049211885
GO:0009986cell surface0.042720417716659
GO:0042803protein homodimerization activity0.0446103001695871
GO:0048869cellular developmental process0.0473024337183543
GO:0030154cell differentiation0.0473024337183543
GO:0016020membrane0.0474945320108906
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds0.0483004518974905
GO:0005768endosome0.0483004518974905
GO:0010324membrane invagination0.0483004518974905
GO:0006897endocytosis0.0483004518974905



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 cell3.07e-118
neuron4.25e-086
neuroblast4.25e-086
electrically signaling cell4.25e-086
neural cell1.62e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system7.64e-8981
nervous system3.31e-8489
neural tube2.64e-8156
neural rod2.64e-8156
future spinal cord2.64e-8156
neural keel2.64e-8156
regional part of nervous system5.44e-7553
regional part of brain5.44e-7553
brain8.20e-6968
future brain8.20e-6968
regional part of forebrain3.41e-6641
forebrain3.41e-6641
anterior neural tube3.41e-6641
future forebrain3.41e-6641
neural plate1.05e-6582
presumptive neural plate1.05e-6582
neurectoderm2.86e-6486
telencephalon1.75e-5634
brain grey matter2.93e-5634
gray matter2.93e-5634
pre-chordal neural plate1.56e-5361
ecto-epithelium2.40e-52104
regional part of telencephalon2.91e-5232
cerebral hemisphere3.08e-5232
adult organism2.30e-49114
ectoderm-derived structure1.16e-45171
ectoderm1.16e-45171
presumptive ectoderm1.16e-45171
regional part of cerebral cortex2.17e-4122
cerebral cortex6.25e-3925
pallium6.25e-3925
structure with developmental contribution from neural crest9.28e-38132
neocortex1.65e-3720
organ system subdivision2.26e-35223
tube1.53e-20192
anatomical cluster1.12e-19373
neural nucleus1.20e-189
nucleus of brain1.20e-189
basal ganglion1.89e-189
nuclear complex of neuraxis1.89e-189
aggregate regional part of brain1.89e-189
collection of basal ganglia1.89e-189
cerebral subcortex1.89e-189
posterior neural tube5.74e-1615
chordal neural plate5.74e-1615
telencephalic nucleus9.15e-157
anatomical conduit2.23e-13240
brainstem3.19e-136
gyrus4.11e-136
organ part1.65e-12218
segmental subdivision of nervous system1.83e-1213
epithelium5.77e-12306
cell layer1.08e-11309
parietal lobe2.63e-115
temporal lobe3.39e-116
occipital lobe4.08e-115
limbic system4.17e-115
embryo4.81e-11592
diencephalon7.49e-117
future diencephalon7.49e-117
segmental subdivision of hindbrain1.27e-1012
hindbrain1.27e-1012
presumptive hindbrain1.27e-1012
germ layer1.40e-10560
germ layer / neural crest1.40e-10560
embryonic tissue1.40e-10560
presumptive structure1.40e-10560
germ layer / neural crest derived structure1.40e-10560
epiblast (generic)1.40e-10560
embryonic structure2.40e-10564
multi-tissue structure5.92e-10342
developing anatomical structure6.59e-10581
regional part of diencephalon2.23e-094
corpus striatum4.84e-094
striatum4.84e-094
ventral part of telencephalon4.84e-094
future corpus striatum4.84e-094
organ1.88e-08503
multi-cellular organism3.27e-08656
anatomical system3.41e-08624
anatomical group3.82e-08625
spinal cord9.88e-083
dorsal region element9.88e-083
dorsum9.88e-083
pons1.40e-073
medulla oblongata2.65e-073
myelencephalon2.65e-073
future myelencephalon2.65e-073
frontal cortex3.78e-073
caudate-putamen4.11e-073
dorsal striatum4.11e-073


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)
MA0003.11.97944
MA0004.10.415381
MA0006.10.733408
MA0007.11.81613
MA0009.10.870971
MA0014.11.50001
MA0017.10.815464
MA0019.10.558663
MA0024.10.766783
MA0025.11.00397
MA0027.12.48103
MA0028.10.280275
MA0029.10.785955
MA0030.10.774581
MA0031.10.710608
MA0038.10.514558
MA0040.10.791764
MA0041.10.433167
MA0042.11.03929
MA0043.10.871285
MA0046.10.860127
MA0048.10.559235
MA0050.10.403421
MA0051.10.510444
MA0052.10.795605
MA0055.11.02363
MA0056.10
MA0057.10.539841
MA0058.10.325084
MA0059.10.323879
MA0060.10.162248
MA0061.11.37555
MA0063.10
MA0066.11.28137
MA0067.11.18766
MA0068.10.109867
MA0069.10.856287
MA0070.10.845142
MA0071.10.47692
MA0072.10.840664
MA0073.10.318422
MA0074.10.509711
MA0076.10.901394
MA0077.10.832987
MA0078.10.607575
MA0081.10.324031
MA0083.10.878452
MA0084.11.37471
MA0087.10.838229
MA0088.10.158781
MA0089.10
MA0090.10.353576
MA0091.10.417885
MA0092.10.381858
MA0093.10.26836
MA0095.10
MA0098.10
MA0100.10.528088
MA0101.10.746654
MA0103.10.257174
MA0105.10.854766
MA0106.11.366
MA0107.11.11943
MA0108.20.707575
MA0109.10
MA0111.10.366362
MA0113.10.57094
MA0114.10.582067
MA0115.11.11137
MA0116.12.50231
MA0117.10.908433
MA0119.10.308914
MA0122.10.934245
MA0124.11.06995
MA0125.10.986127
MA0130.10
MA0131.10.625452
MA0132.10
MA0133.10
MA0135.10.90122
MA0136.10.521435
MA0139.10.406919
MA0140.10.474342
MA0141.10.322254
MA0142.10.679161
MA0143.10.571113
MA0144.10.1885
MA0145.10.177438
MA0146.10.175555
MA0147.10.211483
MA0148.10.439278
MA0149.10.464973
MA0062.20.833414
MA0035.20.473658
MA0039.21.17223
MA0138.20.608783
MA0002.20.905786
MA0137.20.28622
MA0104.20.161609
MA0047.20.542971
MA0112.20.378721
MA0065.21.10761
MA0150.10.34802
MA0151.10
MA0152.11.20819
MA0153.10.969315
MA0154.10.488402
MA0155.10.156896
MA0156.10.288314
MA0157.10.652111
MA0158.10
MA0159.10.60858
MA0160.10.453945
MA0161.10
MA0162.13.32001
MA0163.10.873334
MA0164.10.583138
MA0080.20.268439
MA0018.20.556211
MA0099.20.481058
MA0079.20.893499
MA0102.21.41188
MA0258.10.532421
MA0259.10.218904
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#23512211.13684020245840.01305435313902310.0463105838140772



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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