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{{Coexpression_clusters
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|full_id=C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory
|id=C3308
|ontology_enrichment_celltype=CL:0000055!5.02e-13!180
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000073!2.41e-32!94;UBERON:0001016!2.41e-32!94;UBERON:0001017!7.59e-31!82;UBERON:0005743!9.03e-30!86;UBERON:0000955!4.40e-27!69;UBERON:0006238!4.40e-27!69;UBERON:0001049!2.24e-26!57;UBERON:0005068!2.24e-26!57;UBERON:0006241!2.24e-26!57;UBERON:0007135!2.24e-26!57;UBERON:0002346!9.40e-26!90;UBERON:0000924!5.40e-25!173;UBERON:0006601!5.40e-25!173;UBERON:0002616!2.61e-24!59;UBERON:0003075!3.69e-24!86;UBERON:0007284!3.69e-24!86;UBERON:0004121!1.65e-23!169;UBERON:0000475!3.85e-21!365;UBERON:0003080!2.31e-20!42;UBERON:0007023!4.30e-20!115;UBERON:0002780!5.09e-20!41;UBERON:0001890!5.09e-20!41;UBERON:0006240!5.09e-20!41;UBERON:0000033!7.32e-20!123;UBERON:0002020!1.09e-18!34;UBERON:0003528!1.09e-18!34;UBERON:0001893!2.54e-18!34;UBERON:0001869!2.66e-18!32;UBERON:0000153!3.92e-18!129;UBERON:0007811!3.92e-18!129;UBERON:0002791!9.88e-18!33;UBERON:0003056!1.22e-17!61;UBERON:0002619!7.84e-16!22;UBERON:0000956!1.97e-15!25;UBERON:0000203!1.97e-15!25;UBERON:0000481!4.01e-15!347;UBERON:0001950!1.78e-14!20;UBERON:0000025!2.80e-13!194;UBERON:0000483!1.85e-12!309;UBERON:0000119!2.12e-12!312;UBERON:0004111!2.46e-12!241;UBERON:0000477!4.12e-10!286;UBERON:0000468!7.08e-10!659;UBERON:0000064!6.30e-09!219;UBERON:0000922!7.31e-09!612;UBERON:0002050!4.28e-08!605;UBERON:0005423!4.28e-08!605;UBERON:0000923!7.97e-08!604;UBERON:0005291!7.97e-08!604;UBERON:0006598!7.97e-08!604;UBERON:0002532!7.97e-08!604;UBERON:0003076!3.33e-07!15;UBERON:0003057!3.33e-07!15;UBERON:0000467!8.33e-07!625
}}

Latest revision as of 12:23, 17 September 2013


Full id: C3308_hippocampus_medial_cerebellum_middle_occipital_parietal_olfactory



Phase1 CAGE Peaks

Hg19::chr12:58005170..58005192,+p2@ARHGEF25
Hg19::chr12:58005204..58005235,+p1@ARHGEF25
Hg19::chr12:58005243..58005248,+p3@ARHGEF25


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
non-terminally differentiated cell4.96e-09106
electrically responsive cell8.84e-0761
electrically active cell8.84e-0761
neurectodermal cell8.85e-0759
Uber Anatomy
Ontology termp-valuen
nervous system1.11e-3289
central nervous system5.34e-3081
brain2.80e-2668
future brain2.80e-2668
neural tube5.10e-2656
neural rod5.10e-2656
future spinal cord5.10e-2656
neural keel5.10e-2656
neurectoderm6.78e-2686
ectoderm-derived structure3.71e-25171
ectoderm3.71e-25171
presumptive ectoderm3.71e-25171
regional part of nervous system9.02e-2553
regional part of brain9.02e-2553
neural plate2.65e-2482
presumptive neural plate2.65e-2482
structure with developmental contribution from neural crest1.45e-20132
regional part of forebrain7.38e-2041
forebrain7.38e-2041
anterior neural tube7.38e-2041
future forebrain7.38e-2041
adult organism4.93e-19114
brain grey matter1.90e-1834
gray matter1.90e-1834
anatomical cluster3.08e-18373
cerebral hemisphere5.25e-1832
telencephalon5.47e-1834
organ system subdivision5.77e-18223
ecto-epithelium1.31e-17104
pre-chordal neural plate1.76e-1761
regional part of telencephalon1.87e-1732
regional part of cerebral cortex1.62e-1522
cerebral cortex5.64e-1525
pallium5.64e-1525
multi-tissue structure1.13e-14342
neocortex3.58e-1420
tube1.71e-13192
anatomical conduit3.06e-12240
epithelium4.49e-12306
cell layer5.32e-12309
multi-cellular organism1.72e-10656
organ part1.27e-08218
embryo5.71e-08592
anatomical system1.51e-07624
anatomical group1.88e-07625
posterior neural tube2.35e-0715
chordal neural plate2.35e-0715
germ layer5.52e-07560
germ layer / neural crest5.52e-07560
embryonic tissue5.52e-07560
presumptive structure5.52e-07560
germ layer / neural crest derived structure5.52e-07560
epiblast (generic)5.52e-07560
embryonic structure8.23e-07564


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)
MA0003.12.05336
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.13.14798
MA0017.11.64148
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
MA0048.10.904546
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.16.48547
MA0058.10.716037
MA0059.11.70014
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.11.79391
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.12.3269
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
MA0139.11.12079
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.12.11725
MA0146.17.1063
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.22.74132
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.731309
MA0065.21.39232
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.11.31345
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.12.48891
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.28.15771
MA0102.21.88331
MA0258.10.519674
MA0259.11.40979
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0189478262247415
E2F6#187635.017155731697390.00791769806886330.0320995484885685
HNF4A#3172215.42152690863580.005444210486686610.0246707987598847
ZNF263#1012738.221841637010680.001799043925565870.010906103351647



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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