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{{Coexpression_clusters
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|full_id=C555_cerebellum_pineal_occipital_middle_parietal_medial_locus
|id=C555
|ontology_enrichment_celltype=CL:0000055!6.26e-09!180
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.91e-43!115;UBERON:0000073!7.11e-40!94;UBERON:0001016!7.11e-40!94;UBERON:0005743!7.46e-38!86;UBERON:0001017!1.04e-36!82;UBERON:0002346!8.52e-35!90;UBERON:0003075!1.16e-34!86;UBERON:0007284!1.16e-34!86;UBERON:0001049!2.65e-34!57;UBERON:0005068!2.65e-34!57;UBERON:0006241!2.65e-34!57;UBERON:0007135!2.65e-34!57;UBERON:0000955!1.44e-31!69;UBERON:0006238!1.44e-31!69;UBERON:0002616!1.56e-31!59;UBERON:0000924!1.70e-29!173;UBERON:0006601!1.70e-29!173;UBERON:0004121!5.66e-29!169;UBERON:0003080!6.01e-26!42;UBERON:0000033!8.29e-26!123;UBERON:0002780!1.62e-25!41;UBERON:0001890!1.62e-25!41;UBERON:0006240!1.62e-25!41;UBERON:0000153!3.57e-25!129;UBERON:0007811!3.57e-25!129;UBERON:0003056!4.16e-25!61;UBERON:0000475!5.52e-24!365;UBERON:0002020!2.90e-21!34;UBERON:0003528!2.90e-21!34;UBERON:0001893!3.48e-21!34;UBERON:0002791!1.45e-20!33;UBERON:0000481!2.97e-20!347;UBERON:0001869!5.01e-20!32;UBERON:0000483!3.83e-19!309;UBERON:0000119!8.52e-19!312;UBERON:0000468!6.68e-18!659;UBERON:0000025!2.05e-16!194;UBERON:0000956!8.20e-16!25;UBERON:0000203!8.20e-16!25;UBERON:0000477!1.35e-15!286;UBERON:0002619!1.85e-15!22;UBERON:0004111!2.15e-15!241;UBERON:0001950!3.01e-14!20;UBERON:0000467!3.18e-13!625;UBERON:0000480!6.79e-13!626;UBERON:0000922!1.96e-12!612;UBERON:0000064!4.42e-11!219;UBERON:0002050!6.63e-11!605;UBERON:0005423!6.63e-11!605;UBERON:0000923!1.35e-10!604;UBERON:0005291!1.35e-10!604;UBERON:0006598!1.35e-10!604;UBERON:0002532!1.35e-10!604;UBERON:0000062!1.99e-10!511;UBERON:0003076!2.18e-09!15;UBERON:0003057!2.18e-09!15;UBERON:0004732!3.54e-08!13;UBERON:0004733!1.30e-07!12;UBERON:0002028!1.30e-07!12;UBERON:0007277!1.30e-07!12;UBERON:0002308!6.48e-07!9;UBERON:0000125!6.48e-07!9;UBERON:0002420!7.68e-07!9;UBERON:0007245!7.68e-07!9;UBERON:0010009!7.68e-07!9;UBERON:0010011!7.68e-07!9;UBERON:0000454!7.68e-07!9
}}

Latest revision as of 11:25, 17 September 2013


Full id: C555_cerebellum_pineal_occipital_middle_parietal_medial_locus



Phase1 CAGE Peaks

Hg19::chr10:94000992..94001011,-p@chr10:94000992..94001011
-
Hg19::chr14:27067231..27067247,-p1@NOVA1
Hg19::chr15:61521417..61521460,-p2@RORA
Hg19::chr16:325910..325953,-p1@RGS11
Hg19::chr19:49140692..49140709,-p5@DBP
Hg19::chr19:58566699..58566740,-p@chr19:58566699..58566740
-
Hg19::chr1:204329013..204329086,-p1@PLEKHA6
Hg19::chr1:204654494..204654512,-p4@LRRN2
Hg19::chr22:25202173..25202190,+p3@SGSM1
Hg19::chr22:25202232..25202273,+p2@SGSM1
Hg19::chr22:41956977..41957035,+p2@CSDC2
Hg19::chr3:116164195..116164272,-p2@LSAMP
Hg19::chr6:136847393..136847403,-p15@MAP7
Hg19::chr7:79083072..79083082,-p13@MAGI2
Hg19::chr7:79083088..79083161,-p2@MAGI2
Hg19::chr9:136399759..136399803,+p2@ADAMTSL2


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

p.valueFDRnGenesnPathwayName
6.53560440909036e-050.0413703759095419229Circadian Clock (Reactome):REACT_24941



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><br>uberon_data<br><br>

Uber Anatomy
Ontology termp-valuen
adult organism1.38e-74114
neural tube5.63e-5256
neural rod5.63e-5256
future spinal cord5.63e-5256
neural keel5.63e-5256
nervous system9.45e-5089
central nervous system3.31e-4981
regional part of nervous system6.40e-4953
regional part of brain6.40e-4953
neural plate1.75e-4482
presumptive neural plate1.75e-4482
brain2.84e-4268
future brain2.84e-4268
neurectoderm3.26e-4186
regional part of forebrain2.13e-3741
forebrain2.13e-3741
anterior neural tube2.13e-3741
future forebrain2.13e-3741
organ system subdivision2.75e-35223
structure with developmental contribution from neural crest1.78e-32132
ecto-epithelium4.48e-32104
pre-chordal neural plate1.40e-3061
brain grey matter4.53e-3034
gray matter4.53e-3034
telencephalon5.17e-3034
ectoderm-derived structure6.32e-29171
ectoderm6.32e-29171
presumptive ectoderm6.32e-29171
cerebral hemisphere4.48e-2832
regional part of telencephalon6.29e-2832
anatomical cluster2.92e-23373
regional part of cerebral cortex3.94e-2322
neocortex5.38e-2120
cerebral cortex6.09e-2125
pallium6.09e-2125
multi-tissue structure1.27e-16342
posterior neural tube3.05e-1515
chordal neural plate3.05e-1515
anatomical conduit1.39e-14240
tube5.02e-14192
segmental subdivision of nervous system2.04e-1313
organ6.13e-13503
segmental subdivision of hindbrain2.05e-1212
hindbrain2.05e-1212
presumptive hindbrain2.05e-1212
multi-cellular organism7.12e-12656
organ part3.66e-11218
neural nucleus1.18e-109
nucleus of brain1.18e-109
basal ganglion1.21e-109
nuclear complex of neuraxis1.21e-109
aggregate regional part of brain1.21e-109
collection of basal ganglia1.21e-109
cerebral subcortex1.21e-109
epithelium2.74e-10306
anatomical system5.22e-10624
cell layer6.38e-10309
anatomical group6.51e-10625
regional part of metencephalon2.21e-099
metencephalon2.21e-099
future metencephalon2.21e-099
embryo3.66e-09592
diencephalon8.69e-097
future diencephalon8.69e-097
telencephalic nucleus1.52e-087
gyrus5.32e-086
embryonic structure6.39e-08564
brainstem6.70e-086
germ layer7.35e-08560
germ layer / neural crest7.35e-08560
embryonic tissue7.35e-08560
presumptive structure7.35e-08560
germ layer / neural crest derived structure7.35e-08560
epiblast (generic)7.35e-08560
developing anatomical structure1.53e-07581
parietal lobe6.21e-075
limbic system7.13e-075
occipital lobe8.96e-075


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)
MA0003.13.09978
MA0004.10.238283
MA0006.11.85789
MA0007.11.19118
MA0009.10.644692
MA0014.12.62644
MA0017.10.150184
MA0019.10.359322
MA0024.10.547222
MA0025.10.771296
MA0027.12.23171
MA0028.10.134741
MA0029.10.565022
MA0030.10.554453
MA0031.10.495474
MA0038.10.321141
MA0040.10.570428
MA0041.10.252793
MA0042.10.227947
MA0043.10.644989
MA0046.10.634468
MA0048.13.2561
MA0050.10.228625
MA0051.10.317617
MA0052.10.574006
MA0055.17.01156
MA0056.10
MA0057.11.27784
MA0058.10.5014
MA0059.10.499176
MA0060.10.464905
MA0061.10.0461955
MA0063.10
MA0066.10.321498
MA0067.10.948938
MA0068.11.2688
MA0069.10.630852
MA0070.10.620368
MA0071.10.787225
MA0072.10.616162
MA0073.115.9851
MA0074.10.850035
MA0076.10.178863
MA0077.10.608956
MA0078.10.402443
MA0081.10.166796
MA0083.10.651755
MA0084.11.13204
MA0087.10.613875
MA0088.11.89884
MA0089.10
MA0090.11.0561
MA0091.10.240316
MA0092.10.211423
MA0093.10.397767
MA0095.10
MA0098.10
MA0100.10.332778
MA0101.10.403202
MA0103.10.118522
MA0105.10.16519
MA0106.10.355999
MA0107.10.598395
MA0108.20.492699
MA0109.10
MA0111.10.199239
MA0113.10.968027
MA0114.10.0814649
MA0115.10.874839
MA0116.10.607827
MA0117.10.680135
MA0119.10.471628
MA0122.10.70466
MA0124.10.834787
MA0125.10.75419
MA0130.10
MA0131.10.418384
MA0132.10
MA0133.10
MA0135.10.673296
MA0136.10.327047
MA0139.10.364861
MA0140.10.286995
MA0141.10.165463
MA0142.10.4668
MA0143.10.370225
MA0144.10.546187
MA0145.11.26426
MA0146.10.528155
MA0147.10.617362
MA0148.10.257816
MA0149.11.39788
MA0062.20.0439512
MA0035.20.286421
MA0039.21.09927
MA0138.20.403517
MA0002.20.196222
MA0137.20.138998
MA0104.20.462925
MA0047.20.345656
MA0112.20.22067
MA0065.20.118053
MA0150.10.185024
MA0151.10
MA0152.10.292357
MA0153.10.738108
MA0154.10.820684
MA0155.10.365082
MA0156.10.433955
MA0157.10.442323
MA0158.10
MA0159.10.0884959
MA0160.10.26995
MA0161.10
MA0162.12.09948
MA0163.12.34324
MA0164.10.380804
MA0080.20.126365
MA0018.20.939567
MA0099.20.292649
MA0079.27.06002
MA0102.21.16862
MA0258.10.242841
MA0259.10.640339
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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