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{{Coexpression_clusters
{
|full_id=C1049_pineal_medial_hippocampus_middle_occipital_amygdala_parietal
 

Latest revision as of 11:36, 17 September 2013


Full id: C1049_pineal_medial_hippocampus_middle_occipital_amygdala_parietal



Phase1 CAGE Peaks

Hg19::chr17:38438270..38438296,+p@chr17:38438270..38438296
+
Hg19::chr17:8063552..8063607,-p9@VAMP2
Hg19::chr17:8063738..8063750,-p12@VAMP2
Hg19::chr17:8063830..8063875,-p8@VAMP2
Hg19::chr19:42470916..42470937,-p@chr19:42470916..42470937
-
Hg19::chr1:222791157..222791168,+p10@MIA3
Hg19::chr2:210598049..210598077,+p@chr2:210598049..210598077
+
Hg19::chr2:210598112..210598127,+p@chr2:210598112..210598127
+


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:0002687positive regulation of leukocyte migration0.00185446838572942
GO:0002685regulation of leukocyte migration0.00185446838572942
GO:0030335positive regulation of cell migration0.0107107636356278
GO:0030336negative regulation of cell migration0.0107107636356278
GO:0051272positive regulation of cell motility0.0107107636356278
GO:0040017positive regulation of locomotion0.0107107636356278
GO:0051271negative regulation of cell motility0.0107107636356278
GO:0040013negative regulation of locomotion0.0107107636356278
GO:0007162negative regulation of cell adhesion0.0107107636356278
GO:0050900leukocyte migration0.011492627144804
GO:0019717synaptosome0.012132085517086
GO:0030334regulation of cell migration0.0169040912870174
GO:0030155regulation of cell adhesion0.0169040912870174
GO:0051270regulation of cell motility0.0169040912870174
GO:0040012regulation of locomotion0.0169040912870174
GO:0040011locomotion0.0169040912870174
GO:0002684positive regulation of immune system process0.0187393830162024
GO:0002682regulation of immune system process0.0204653811019412
GO:0051240positive regulation of multicellular organismal process0.0204653811019412
GO:0042060wound healing0.0242470526812193
GO:0016477cell migration0.0410110173448688
GO:0051239regulation of multicellular organismal process0.0465091813705923
GO:0051179localization0.0476470727683483



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 tube1.28e-5056
neural rod1.28e-5056
future spinal cord1.28e-5056
neural keel1.28e-5056
regional part of nervous system5.03e-4753
regional part of brain5.03e-4753
central nervous system1.69e-4481
nervous system7.45e-4489
neural plate1.88e-4182
presumptive neural plate1.88e-4182
brain2.12e-4068
future brain2.12e-4068
regional part of forebrain2.27e-4041
forebrain2.27e-4041
anterior neural tube2.27e-4041
future forebrain2.27e-4041
neurectoderm3.58e-4086
adult organism2.99e-35114
ecto-epithelium8.00e-34104
brain grey matter1.78e-3234
gray matter1.78e-3234
telencephalon3.71e-3234
pre-chordal neural plate1.64e-3061
cerebral hemisphere3.19e-3032
regional part of telencephalon4.03e-3032
regional part of cerebral cortex2.68e-2622
structure with developmental contribution from neural crest6.25e-26132
ectoderm-derived structure2.32e-24171
ectoderm2.32e-24171
presumptive ectoderm2.32e-24171
neocortex1.11e-2320
cerebral cortex3.05e-2225
pallium3.05e-2225
organ system subdivision1.36e-16223
basal ganglion5.36e-129
nuclear complex of neuraxis5.36e-129
aggregate regional part of brain5.36e-129
collection of basal ganglia5.36e-129
cerebral subcortex5.36e-129
neural nucleus8.33e-129
nucleus of brain8.33e-129
tube1.17e-11192
posterior neural tube2.98e-1115
chordal neural plate2.98e-1115
diencephalon1.27e-097
future diencephalon1.27e-097
telencephalic nucleus1.74e-097
segmental subdivision of nervous system5.56e-0913
organ part6.98e-09218
gyrus8.81e-096
brainstem3.51e-086
anatomical cluster4.23e-08373
segmental subdivision of hindbrain4.38e-0812
hindbrain4.38e-0812
presumptive hindbrain4.38e-0812
limbic system7.80e-085
occipital lobe1.03e-075
anatomical conduit1.30e-07240
epithelium2.06e-07306
temporal lobe2.23e-076
parietal lobe2.71e-075
cell layer3.85e-07309


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)
MA0003.10.00718652
MA0004.10.455723
MA0006.10.300178
MA0007.10.437331
MA0009.10.918715
MA0014.10.275152
MA0017.11.60885
MA0019.10.602411
MA0024.10.813542
MA0025.11.05265
MA0027.12.5321
MA0028.10.846854
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
MA0048.10.0955945
MA0050.10.443405
MA0051.11.36251
MA0052.10.842664
MA0055.10.118169
MA0056.10
MA0057.10.305162
MA0058.10.362328
MA0059.10.948176
MA0060.10.190336
MA0061.10.165998
MA0063.10
MA0066.12.35092
MA0067.11.23721
MA0068.10.823119
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
MA0090.11.79681
MA0091.11.16006
MA0092.10.421159
MA0093.10.303084
MA0095.10
MA0098.10
MA0100.10.571227
MA0101.10.825856
MA0103.10.792149
MA0105.10.0818021
MA0106.10.59853
MA0107.10.236528
MA0108.20.753643
MA0109.10
MA0111.10.405141
MA0113.10.614917
MA0114.11.89851
MA0115.12.61199
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
MA0135.10.949204
MA0136.10.564434
MA0139.10.155155
MA0140.10.516266
MA0141.10.359385
MA0142.10.724856
MA0143.10.615094
MA0144.10.218541
MA0145.10.0613434
MA0146.10.113833
MA0147.10.243042
MA0148.10.480298
MA0149.14.35441
MA0062.20.161302
MA0035.20.515566
MA0039.20.284736
MA0138.20.653421
MA0002.20.531206
MA0137.20.321796
MA0104.20.189646
MA0047.20.586412
MA0112.20.0572179
MA0065.21.78056
MA0150.10.386144
MA0151.10
MA0152.10.52279
MA0153.11.01778
MA0154.10.0799828
MA0155.10.0535085
MA0156.10.323987
MA0157.10.697424
MA0158.10
MA0159.11.26616
MA0160.11.23953
MA0161.10
MA0162.10.0752715
MA0163.10.493198
MA0164.10.627336
MA0080.20.303167
MA0018.20.599912
MA0099.20.523145
MA0079.20.277508
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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