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{{Coexpression_clusters
{
|full_id=C1022_Ciliary_Lens_Astrocyte_Neural_Iris_retina_Hair
 

Latest revision as of 11:36, 17 September 2013


Full id: C1022_Ciliary_Lens_Astrocyte_Neural_Iris_retina_Hair



Phase1 CAGE Peaks

Hg19::chr12:97856211..97856221,+p@chr12:97856211..97856221
+
Hg19::chr2:210798666..210798677,+p@chr2:210798666..210798677
+
Hg19::chr2:45166478..45166502,-p3@ENST00000437916
Hg19::chr2:45166504..45166533,-p2@ENST00000437916
Hg19::chr3:173116225..173116242,+p10@NLGN1
Hg19::chr3:8536114..8536125,-p@chr3:8536114..8536125
-
Hg19::chr7:115723897..115723915,-p@chr7:115723897..115723915
-
Hg19::chr7:115723925..115723935,-p@chr7:115723925..115723935
-


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:0016080synaptic vesicle targeting0.00459201695513952
GO:0042043neurexin binding0.00459201695513952
GO:0016079synaptic vesicle exocytosis0.00459201695513952
GO:0006903vesicle targeting0.00459201695513952
GO:0051650establishment of vesicle localization0.00459201695513952
GO:0051648vesicle localization0.00459201695513952
GO:0048489synaptic vesicle transport0.00542692912880125
GO:0051656establishment of organelle localization0.00542692912880125
GO:0016339calcium-dependent cell-cell adhesion0.00542692912880125
GO:0007416synaptogenesis0.00542692912880125
GO:0045664regulation of neuron differentiation0.00542692912880125
GO:0051640organelle localization0.00631402331331684
GO:0050808synapse organization and biogenesis0.00656002422162789
GO:0007269neurotransmitter secretion0.00656002422162789
GO:0045055regulated secretory pathway0.00811256328741317
GO:0003001generation of a signal involved in cell-cell signaling0.0100450370893677
GO:0001505regulation of neurotransmitter levels0.0105346271323789
GO:0043062extracellular structure organization and biogenesis0.0107147062286589
GO:0006887exocytosis0.0134135232110655
GO:0045595regulation of cell differentiation0.0162907268170426
GO:0045211postsynaptic membrane0.0162907268170426
GO:0044456synapse part0.0168026074949424
GO:0030182neuron differentiation0.0205790389471068
GO:0006605protein targeting0.0205790389471068
GO:0050793regulation of developmental process0.0205790389471068
GO:0045045secretory pathway0.0205790389471068
GO:0048699generation of neurons0.0205790389471068
GO:0022008neurogenesis0.0214840793258313
GO:0007268synaptic transmission0.0227304839279407
GO:0032940secretion by cell0.0227304839279407
GO:0007017microtubule-based process0.0233304087236927
GO:0019226transmission of nerve impulse0.0236775874249382
GO:0016337cell-cell adhesion0.0241428770217184
GO:0046903secretion0.0259313898643173
GO:0030054cell junction0.0281425039107837
GO:0006886intracellular protein transport0.0337385690176223
GO:0016192vesicle-mediated transport0.037604895605602
GO:0007267cell-cell signaling0.0386696164643328
GO:0007010cytoskeleton organization and biogenesis0.0403862004003297
GO:0007399nervous system development0.0410985517484988
GO:0015031protein transport0.0479666118900987
GO:0046907intracellular transport0.0479666118900987
GO:0045184establishment of protein localization0.0479666118900987
GO:0022610biological adhesion0.0479666118900987
GO:0007155cell adhesion0.0479666118900987
GO:0008104protein localization0.0479666118900987
GO:0033036macromolecule localization0.0494374591340553



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>

Uber Anatomy
Ontology termp-valuen
atypical epithelium4.11e-674
pigment epithelium of eye3.17e-5411
ciliary epithelium5.78e-513
ciliary body5.78e-513
eye6.45e-5021
visual system6.45e-5021
vasculature of eye5.94e-456
uvea5.94e-456
vasculature of head5.94e-456
sense organ1.21e-4324
sensory system1.21e-4324
entire sense organ system1.21e-4324
anterior segment of eyeball1.26e-4214
camera-type eye2.30e-4020
simple eye2.30e-4020
immature eye2.30e-4020
ocular region2.30e-4020
eyeball of camera-type eye2.30e-4020
optic cup2.30e-4020
optic vesicle2.30e-4020
eye primordium2.30e-4020
face1.11e-3622
ectodermal placode5.66e-2631
vasculature of organ9.32e-2511
iris epithelium5.26e-181
iris5.26e-181
cuboidal epithelium1.57e-174
transparent eye structure1.57e-174
simple cuboidal epithelium1.57e-174
cranial placode1.57e-174
lens of camera-type eye1.57e-174
epithelium of lens1.57e-174
lens placode1.57e-174
lens vesicle1.57e-174
pre-chordal neural plate1.14e-1661
subdivision of head2.51e-1649
head3.05e-1456
anterior region of body7.92e-1362
craniocervical region7.92e-1362
neural plate2.58e-1282
presumptive neural plate2.58e-1282
neurectoderm1.01e-1186
ecto-epithelium1.31e-09104
external ectoderm3.01e-098
organ segment5.89e-0898
structure with developmental contribution from neural crest1.89e-07132
ectoderm-derived structure5.02e-07171
ectoderm5.02e-07171
presumptive ectoderm5.02e-07171


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)
MA0003.10.0264723
MA0004.10.455723
MA0006.10.812175
MA0007.10.437331
MA0009.10.918715
MA0014.10.00962431
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
MA0046.12.0979
MA0048.10.0955945
MA0050.10.443405
MA0051.10.553205
MA0052.10.842664
MA0055.10.118169
MA0056.10
MA0057.11.05663
MA0058.10.362328
MA0059.10.361075
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.10.557833
MA0067.11.23721
MA0068.11.93074
MA0069.10.903908
MA0070.10.892666
MA0071.10.518907
MA0072.10.888148
MA0073.10.466265
MA0074.10.552456
MA0076.10.377799
MA0077.10.880402
MA0078.10.652193
MA0081.10.948525
MA0083.10.926258
MA0084.11.42483
MA0087.10.885691
MA0088.10.054222
MA0089.10
MA0090.10.391903
MA0091.10.458301
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.30624
MA0103.10.291333
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.11.22129
MA0115.11.1606
MA0116.10.239768
MA0117.10.956472
MA0119.10.345493
MA0122.10.982472
MA0124.11.11898
MA0125.11.0347
MA0130.10
MA0131.10.670358
MA0132.10
MA0133.10
MA0135.12.18252
MA0136.10.564434
MA0139.10.916926
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.220937
MA0146.10.00761723
MA0147.10.681318
MA0148.10.480298
MA0149.12.18301
MA0062.20.161302
MA0035.20.515566
MA0039.20.0817047
MA0138.20.653421
MA0002.21.01797
MA0137.20.321796
MA0104.20.55506
MA0047.20.586412
MA0112.20.0572179
MA0065.20.490252
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.12.32222
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.10.682702
MA0160.10.495355
MA0161.10
MA0162.10.378102
MA0163.10.141536
MA0164.11.51849
MA0080.20.303167
MA0018.20.599912
MA0099.21.29876
MA0079.20.754308
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.

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