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{{Coexpression_clusters
{
|full_id=C286_cerebellum_occipital_optic_parietal_globus_caudate_medial

Latest revision as of 11:14, 17 September 2013


Full id: C286_cerebellum_occipital_optic_parietal_globus_caudate_medial



Phase1 CAGE Peaks

Hg19::chr12:2944396..2944456,-p2@NRIP2
Hg19::chr15:31770272..31770297,-p1@LOC283713
Hg19::chr15:41576157..41576168,+p1@ENST00000558457
p1@ENST00000558945
Hg19::chr15:68871151..68871206,+p4@CORO2B
Hg19::chr15:83349215..83349224,-p6@AP3B2
Hg19::chr17:77086942..77086969,-p@chr17:77086942..77086969
-
Hg19::chr19:35630530..35630544,+p8@FXYD1
Hg19::chr19:6496061..6496072,-p@chr19:6496061..6496072
-
Hg19::chr2:39944930..39944941,+p@chr2:39944930..39944941
+
Hg19::chr7:127807707..127807735,+p@chr7:127807707..127807735
+
Hg19::chr7:78995180..78995184,-p@chr7:78995180..78995184
-
Hg19::chrX:139865330..139865375,+p3@AK054921
Hg19::chrX:139865378..139865502,+p2@AK054921
Hg19::chrX:139865504..139865511,+p9@AK054921
Hg19::chrX:139865512..139865534,+p5@AK054921
Hg19::chrX:139865537..139865548,+p8@AK054921
Hg19::chrX:139865549..139865571,+p4@AK054921
Hg19::chrX:139865584..139865721,+p1@AK054921
Hg19::chrX:139865729..139865742,+p7@AK054921
Hg19::chrX:139865777..139865788,+p10@AK054921
Hg19::chrX:139865816..139865840,+p6@AK054921
Hg19::chrX:139865845..139865894,+p@chrX:139865845..139865894
+
Hg19::chrX:139865901..139865949,+p@chrX:139865901..139865949
+
Hg19::chrX:139865951..139865954,+p@chrX:139865951..139865954
+
Hg19::chrX:139865977..139866003,+p@chrX:139865977..139866003
+
Hg19::chrX:139866014..139866036,+p@chrX:139866014..139866036
+
Hg19::chrX:139866041..139866089,+p@chrX:139866041..139866089
+
Hg19::chrX:139866092..139866140,+p@chrX:139866092..139866140
+
Hg19::chrX:139866145..139866181,+p@chrX:139866145..139866181
+
Hg19::chrX:139866182..139866193,+p@chrX:139866182..139866193
+
Hg19::chrX:139866201..139866208,+p@chrX:139866201..139866208
+
Hg19::chrX:139866235..139866251,+p@chrX:139866235..139866251
+
Hg19::chrX:139866285..139866318,+p@chrX:139866285..139866318
+
Hg19::chrX:139866325..139866336,+p@chrX:139866325..139866336
+
Hg19::chrX:139866361..139866428,+p@chrX:139866361..139866428
+
Hg19::chrX:139866444..139866469,+p@chrX:139866444..139866469
+
Hg19::chrX:139866474..139866484,+p@chrX:139866474..139866484
+
Hg19::chrX:139866489..139866516,+p@chrX:139866489..139866516
+
Hg19::chrX:139866541..139866552,+p@chrX:139866541..139866552
+
Hg19::chrX:139866560..139866578,+p@chrX:139866560..139866578
+
Hg19::chrX:139866580..139866589,+p@chrX:139866580..139866589
+
Hg19::chrX:139866595..139866724,+p@chrX:139866595..139866724
+
Hg19::chrX:139866734..139866760,+p@chrX:139866734..139866760
+
Hg19::chrX:139866762..139866765,+p@chrX:139866762..139866765
+
Hg19::chrX:139866776..139866793,+p@chrX:139866776..139866793
+


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

No GOStat results

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
fat cell2.59e-1015
Uber Anatomy
Ontology termp-valuen
adult organism2.09e-42114
neural tube3.90e-3956
neural rod3.90e-3956
future spinal cord3.90e-3956
neural keel3.90e-3956
regional part of nervous system1.75e-3653
regional part of brain1.75e-3653
neurectoderm5.83e-3486
central nervous system1.97e-3381
neural plate5.01e-3382
presumptive neural plate5.01e-3382
nervous system4.58e-3289
regional part of forebrain3.12e-3141
forebrain3.12e-3141
anterior neural tube3.12e-3141
future forebrain3.12e-3141
brain6.71e-2968
future brain6.71e-2968
brain grey matter3.77e-2834
gray matter3.77e-2834
telencephalon5.63e-2834
structure with developmental contribution from neural crest2.27e-26132
regional part of telencephalon3.16e-2632
cerebral hemisphere4.15e-2632
ecto-epithelium8.48e-24104
pre-chordal neural plate1.11e-2361
regional part of cerebral cortex4.18e-2222
ectoderm-derived structure2.63e-20171
ectoderm2.63e-20171
presumptive ectoderm2.63e-20171
neocortex2.74e-2020
cerebral cortex1.33e-1925
pallium1.33e-1925
organ system subdivision4.71e-18223
multi-tissue structure3.66e-14342
anatomical cluster3.95e-13373
tube8.78e-11192
epithelium1.47e-10306
anatomical conduit1.92e-10240
cell layer3.83e-10309
neural nucleus4.39e-109
nucleus of brain4.39e-109
multi-cellular organism5.35e-10656
basal ganglion7.10e-109
nuclear complex of neuraxis7.10e-109
aggregate regional part of brain7.10e-109
collection of basal ganglia7.10e-109
cerebral subcortex7.10e-109
posterior neural tube4.72e-0915
chordal neural plate4.72e-0915
organ part1.51e-08218
telencephalic nucleus3.37e-087
germ layer6.77e-08560
germ layer / neural crest6.77e-08560
embryonic tissue6.77e-08560
presumptive structure6.77e-08560
germ layer / neural crest derived structure6.77e-08560
epiblast (generic)6.77e-08560
embryonic structure6.88e-08564
segmental subdivision of nervous system1.36e-0713
temporal lobe1.39e-076
gyrus4.05e-076
brainstem6.04e-076


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)
MA0003.15.19629e-06
MA0004.10.156843
MA0006.10.0449853
MA0007.10.0350407
MA0009.10.288527
MA0014.19.88117e-06
MA0017.10.0656573
MA0019.10.0961252
MA0024.10.215619
MA0025.10.390923
MA0027.11.78493
MA0028.12.30121
MA0029.10.228475
MA0030.10.220816
MA0031.10.179572
MA0038.11.41746
MA0040.10.656559
MA0041.10.174338
MA0042.10.144754
MA0043.10.288758
MA0046.10.280609
MA0048.10.0946971
MA0050.10.0367154
MA0051.10.0746188
MA0052.10.235047
MA0055.10.024447
MA0056.10
MA0057.10.000388982
MA0058.10.657612
MA0059.10.969725
MA0060.10.00128055
MA0061.10.000686528
MA0063.10
MA0066.10.0765267
MA0067.10.54503
MA0068.10.000242346
MA0069.10.277823
MA0070.12.0969
MA0071.10.0612473
MA0072.10.266579
MA0073.18.58751e-11
MA0074.10.0743125
MA0076.10.0209784
MA0077.10.261111
MA0078.10.120524
MA0081.10.0178127
MA0083.10.294032
MA0084.10.71238
MA0087.10.26484
MA0088.10.00864099
MA0089.10
MA0090.10.023927
MA0091.10.159257
MA0092.11.70098
MA0093.10.12924
MA0095.10
MA0098.10
MA0100.10.0821839
MA0101.11.77529
MA0103.10.242703
MA0105.10.00129462
MA0106.10.0943326
MA0107.10.144
MA0108.20.177698
MA0109.10
MA0111.10.112964
MA0113.10.102012
MA0114.10.0592346
MA0115.10.479539
MA0116.10.0208303
MA0117.10.316417
MA0119.10.0150966
MA0122.10.336089
MA0124.10.444822
MA0125.10.982538
MA0130.10
MA0131.10.130054
MA0132.10
MA0133.10
MA0135.10.310984
MA0136.10.0792895
MA0139.10.0432966
MA0140.10.0602746
MA0141.10.0174792
MA0142.10.160525
MA0143.10.102096
MA0144.1142.917
MA0145.10.00502041
MA0146.10.000148062
MA0147.10.0684386
MA0148.10.0478476
MA0149.10.0568069
MA0062.20.191798
MA0035.20.060018
MA0039.21.31136e-07
MA0138.20.121158
MA0002.20.000989777
MA0137.2119.501
MA0104.20.0786553
MA0047.20.08884
MA0112.20.010333
MA0065.20.0142369
MA0150.10.0226948
MA0151.10
MA0152.10.0626927
MA0153.10.363372
MA0154.10.000211674
MA0155.10.000907333
MA0156.16.53468
MA0157.10.144843
MA0158.10
MA0159.10.0220537
MA0160.10.0528624
MA0161.10
MA0162.14.84035e-06
MA0163.13.10553e-06
MA0164.10.10802
MA0080.20.00914139
MA0018.20.094969
MA0099.20.0628256
MA0079.20
MA0102.20.74655
MA0258.10.0433046
MA0259.10.729731
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

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