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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:26, 17 September 2013


Full id: C586_cerebellum_brain_occipital_middle_parietal_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr11:132807611..132807618,-p@chr11:132807611..132807618
-
Hg19::chr11:132814188..132814199,-p@chr11:132814188..132814199
-
Hg19::chr13:102746160..102746164,-p@chr13:102746160..102746164
-
Hg19::chr16:6493692..6493697,+p@chr16:6493692..6493697
+
Hg19::chr17:884354..884374,-p@chr17:884354..884374
-
Hg19::chr19:13317729..13317738,-p@chr19:13317729..13317738
-
Hg19::chr1:18433873..18433888,+p8@IGSF21
Hg19::chr20:33815160..33815166,-p@chr20:33815160..33815166
-
Hg19::chr22:51158914..51158921,+p13@SHANK3
Hg19::chr5:160820302..160820306,-p@chr5:160820302..160820306
-
Hg19::chr5:176256892..176256896,+p@chr5:176256892..176256896
+
Hg19::chr7:153634554..153634556,+p@chr7:153634554..153634556
+
Hg19::chr7:36561860..36561869,-p@chr7:36561860..36561869
-
Hg19::chr8:9776684..9776691,-p@chr8:9776684..9776691
-
Hg19::chr9:114312975..114312986,+p@chr9:114312975..114312986
+


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:0001838embryonic epithelial tube formation0.0187743671962285
GO:0016331morphogenesis of embryonic epithelium0.0187743671962285
GO:0002009morphogenesis of an epithelium0.0304695680059167
GO:0035239tube morphogenesis0.0304695680059167
GO:0048598embryonic morphogenesis0.0304695680059167
GO:0035295tube development0.0304695680059167
GO:0045211postsynaptic membrane0.0304695680059167
GO:0000165MAPKKK cascade0.0304695680059167
GO:0044456synapse part0.0304695680059167
GO:0009790embryonic development0.0399830940917626



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
regional part of nervous system4.19e-7253
regional part of brain4.19e-7253
neural tube4.24e-6856
neural rod4.24e-6856
future spinal cord4.24e-6856
neural keel4.24e-6856
brain7.62e-6568
future brain7.62e-6568
cerebral hemisphere2.35e-5932
telencephalon8.74e-5634
brain grey matter9.70e-5634
gray matter9.70e-5634
central nervous system4.85e-5481
regional part of telencephalon2.04e-5232
regional part of forebrain9.30e-5241
forebrain9.30e-5241
anterior neural tube9.30e-5241
future forebrain9.30e-5241
regional part of cerebral cortex2.09e-5022
nervous system2.40e-4889
neocortex4.47e-4720
neural plate1.68e-4582
presumptive neural plate1.68e-4582
cerebral cortex2.54e-4425
pallium2.54e-4425
neurectoderm3.20e-4386
ecto-epithelium4.17e-35104
adult organism6.22e-35114
pre-chordal neural plate5.59e-3461
gyrus9.77e-306
structure with developmental contribution from neural crest1.91e-29132
ectoderm-derived structure1.52e-23171
ectoderm1.52e-23171
presumptive ectoderm1.52e-23171
segmental subdivision of hindbrain4.67e-2112
hindbrain4.67e-2112
presumptive hindbrain4.67e-2112
segmental subdivision of nervous system2.10e-1913
brainstem7.00e-196
organ system subdivision1.09e-18223
tube3.59e-17192
temporal lobe7.79e-176
posterior neural tube9.33e-1715
chordal neural plate9.33e-1715
corpus striatum1.92e-164
striatum1.92e-164
ventral part of telencephalon1.92e-164
future corpus striatum1.92e-164
middle temporal gyrus2.08e-152
limbic system1.07e-135
parietal lobe2.03e-135
organ part3.69e-13218
regional part of metencephalon3.89e-139
metencephalon3.89e-139
future metencephalon3.89e-139
basal ganglion6.42e-139
nuclear complex of neuraxis6.42e-139
aggregate regional part of brain6.42e-139
collection of basal ganglia6.42e-139
cerebral subcortex6.42e-139
anatomical conduit6.90e-13240
neural nucleus9.32e-139
nucleus of brain9.32e-139
frontal cortex1.22e-103
caudate-putamen2.38e-103
dorsal striatum2.38e-103
medulla oblongata2.49e-103
myelencephalon2.49e-103
future myelencephalon2.49e-103
pons2.88e-103
telencephalic nucleus1.25e-097
anatomical cluster2.01e-09373
epithelium3.61e-09306
cell layer4.89e-09309
olfactory region1.02e-081
primary subdivision of skull1.02e-081
cranium1.02e-081
neurocranium1.02e-081
chondrocranium1.02e-081
cartilaginous neurocranium1.02e-081
head paraxial mesoderm1.02e-081
multi-tissue structure1.15e-08342
insula1.18e-081
paracentral gyrus1.59e-081
putamen1.84e-081
nucleus accumbens2.13e-081
ventral striatum2.13e-081
occipital pole3.06e-081
pole of cerebral hemisphere3.06e-081
postcentral gyrus3.53e-081


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)
MA0003.10.0132214
MA0004.10.256222
MA0006.10.137644
MA0007.10.67744
MA0009.10.669377
MA0014.10.240828
MA0017.10.16476
MA0019.10.38027
MA0024.10.570967
MA0025.10.796882
MA0027.12.25966
MA0028.10.148561
MA0029.10.588958
MA0030.10.578277
MA0031.10.518602
MA0038.10.904297
MA0040.10.594421
MA0041.10.746198
MA0042.10.245557
MA0043.10.669676
MA0046.10.659066
MA0048.10.23222
MA0050.10.246257
MA0051.10.337676
MA0052.10.598036
MA0055.10.579321
MA0056.10
MA0057.10.420982
MA0058.10.182945
MA0059.10.182001
MA0060.10.237888
MA0061.10.198509
MA0063.10
MA0066.10.341645
MA0067.10.975379
MA0068.10.341559
MA0069.10.655419
MA0070.10.644843
MA0071.10.308534
MA0072.10.640598
MA0073.13.30649
MA0074.10.337035
MA0076.10.194691
MA0077.10.633326
MA0078.10.424186
MA0081.10.18212
MA0083.10.676499
MA0084.11.15904
MA0087.11.54141
MA0088.10.0411204
MA0089.10
MA0090.10.593146
MA0091.10.716673
MA0092.11.2087
MA0093.10.139688
MA0095.10
MA0098.10
MA0100.10.930697
MA0101.10.141917
MA0103.10.131472
MA0105.10.074747
MA0106.10.37688
MA0107.10.315431
MA0108.20.515791
MA0109.10
MA0111.10.215855
MA0113.10.39123
MA0114.10.0920489
MA0115.10.900969
MA0116.10.320986
MA0117.10.705104
MA0119.10.170362
MA0122.10.729811
MA0124.10.860724
MA0125.10.779672
MA0130.10
MA0131.10.440395
MA0132.10
MA0133.10
MA0135.10.698212
MA0136.10.347318
MA0139.10.181369
MA0140.10.30631
MA0141.10.180729
MA0142.10.489543
MA0143.10.391385
MA0144.10.0838502
MA0145.10.7339
MA0146.10.114035
MA0147.10.326612
MA0148.10.276339
MA0149.10.298252
MA0062.20.0512998
MA0035.20.824687
MA0039.20.072333
MA0138.20.425279
MA0002.20.82964
MA0137.20.153033
MA0104.20.0667907
MA0047.20.366327
MA0112.20.0445156
MA0065.20.140846
MA0150.10.201098
MA0151.10
MA0152.10.311809
MA0153.10.763487
MA0154.10.187751
MA0155.10.11478
MA0156.10.154615
MA0157.10.46471
MA0158.10
MA0159.10.327637
MA0160.10.288813
MA0161.10
MA0162.10.374202
MA0163.10.393441
MA0164.10.402162
MA0080.20.139746
MA0018.20.378086
MA0099.20.312108
MA0079.20.0966405
MA0102.21.1957
MA0258.10.0785319
MA0259.10.104286
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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