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{{Coexpression_clusters
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follicle development!0.0114354058803748!7425$GO:0016524!latrotoxin receptor activity!0.0114354058803748!10439$GO:0022601!menstrual cycle phase!0.0114354058803748!7425$GO:0022602!menstrual cycle process!0.0114354058803748!7425$GO:0008585!female gonad development!0.0114354058803748!7425$GO:0046660!female sex differentiation!0.0114354058803748!7425$GO:0046545!development of primary female sexual characteristics!0.0114354058803748!7425$GO:0042698!menstrual cycle!0.0114354058803748!7425$GO:0005184!neuropeptide hormone activity!0.0114354058803748!7425$GO:0048731!system development!0.0117358057120867!7425;10439$GO:0008406!gonad development!0.0117358057120867!7425$GO:0048608!reproductive structure development!0.0117358057120867!7425$GO:0048856!anatomical structure development!0.0117358057120867!7425;10439$GO:0045137!development of primary sexual characteristics!0.0117358057120867!7425$GO:0032504!multicellular organism reproduction!0.0117358057120867!7425$GO:0048609!reproductive process in a 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|full_id=C4634_melanoma_occipital_amygdala_temporal_postcentral_brain_insula
|id=C4634
}}

Latest revision as of 14:16, 17 September 2013


Full id: C4634_melanoma_occipital_amygdala_temporal_postcentral_brain_insula



Phase1 CAGE Peaks

Hg19::chr7:100808320..100808338,-p3@VGF
Hg19::chr7:100808394..100808436,-p2@VGF
Hg19::chr9:137967395..137967412,+p2@OLFM1


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:0001541ovarian follicle development0.0114354058803748
GO:0016524latrotoxin receptor activity0.0114354058803748
GO:0022601menstrual cycle phase0.0114354058803748
GO:0022602menstrual cycle process0.0114354058803748
GO:0008585female gonad development0.0114354058803748
GO:0046660female sex differentiation0.0114354058803748
GO:0046545development of primary female sexual characteristics0.0114354058803748
GO:0042698menstrual cycle0.0114354058803748
GO:0005184neuropeptide hormone activity0.0114354058803748
GO:0048731system development0.0117358057120867
GO:0008406gonad development0.0117358057120867
GO:0048608reproductive structure development0.0117358057120867
GO:0048856anatomical structure development0.0117358057120867
GO:0045137development of primary sexual characteristics0.0117358057120867
GO:0032504multicellular organism reproduction0.0117358057120867
GO:0048609reproductive process in a multicellular organism0.0117358057120867
GO:0005788endoplasmic reticulum lumen0.0117358057120867
GO:0007275multicellular organismal development0.0132863134972843
GO:0007548sex differentiation0.0132863134972843
GO:0003006reproductive developmental process0.013555761989149
GO:0032502developmental process0.0244911273801044
GO:0032501multicellular organismal process0.0293449752098031
GO:0005179hormone activity0.0293449752098031
GO:0008083growth factor activity0.0327702848493947
GO:0022414reproductive process0.0362342900506413
GO:0044444cytoplasmic part0.0362342900506413
GO:0019953sexual reproduction0.0362342900506413
GO:0031410cytoplasmic vesicle0.0461856130606856
GO:0031982vesicle0.0461856130606856



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>disease_data<br>

Cell Type
Ontology termp-valuen
neuron6.05e-126
neuroblast6.05e-126
electrically signaling cell6.05e-126
neuronal stem cell1.35e-118
embryonic stem cell4.20e-105
Uber Anatomy
Ontology termp-valuen
central nervous system2.33e-6581
nervous system2.65e-6489
neural tube3.17e-6056
neural rod3.17e-6056
future spinal cord3.17e-6056
neural keel3.17e-6056
regional part of nervous system2.23e-5853
regional part of brain2.23e-5853
regional part of forebrain4.25e-5441
forebrain4.25e-5441
anterior neural tube4.25e-5441
future forebrain4.25e-5441
cerebral hemisphere9.64e-5232
telencephalon1.48e-5134
brain grey matter3.63e-5134
gray matter3.63e-5134
brain1.27e-4968
future brain1.27e-4968
regional part of telencephalon7.48e-4832
neurectoderm4.64e-4486
regional part of cerebral cortex1.60e-4322
neural plate9.26e-4182
presumptive neural plate9.26e-4182
neocortex2.44e-3920
cerebral cortex1.18e-3725
pallium1.18e-3725
pre-chordal neural plate5.24e-3761
ectoderm-derived structure6.79e-35171
ectoderm6.79e-35171
presumptive ectoderm6.79e-35171
ecto-epithelium7.17e-33104
adult organism2.88e-26114
structure with developmental contribution from neural crest8.01e-23132
organ system subdivision1.03e-19223
basal ganglion1.69e-159
nuclear complex of neuraxis1.69e-159
aggregate regional part of brain1.69e-159
collection of basal ganglia1.69e-159
cerebral subcortex1.69e-159
neural nucleus1.06e-149
nucleus of brain1.06e-149
gyrus1.08e-136
limbic system5.58e-125
temporal lobe1.21e-116
parietal lobe1.27e-115
telencephalic nucleus1.62e-117
occipital lobe2.00e-115
brainstem2.35e-116
tube2.85e-10192
corpus striatum5.09e-104
striatum5.09e-104
ventral part of telencephalon5.09e-104
future corpus striatum5.09e-104
posterior neural tube9.87e-0915
chordal neural plate9.87e-0915
caudate-putamen6.57e-083
dorsal striatum6.57e-083
frontal cortex1.30e-073
anatomical cluster1.88e-07373
segmental subdivision of hindbrain5.84e-0712
hindbrain5.84e-0712
presumptive hindbrain5.84e-0712
Disease
Ontology termp-valuen
germ cell and embryonal cancer9.74e-1022
germ cell cancer9.74e-1022
neuroectodermal tumor2.57e-0810


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)
MA0003.10.708947
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.118426
MA0017.10.686276
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
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.12.01615
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.10.211629
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
MA0089.10
MA0090.10.751469
MA0091.11.93651
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.13.21605
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
MA0145.12.11725
MA0146.10.348055
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.757898
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.711948
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.13.52399
MA0163.11.2663
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.941469
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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.

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