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Coexpression cluster:C2222

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Full id: C2222_caudate_globus_thalamus_medial_amygdala_putamen_parietal



Phase1 CAGE Peaks

Hg19::chr12:57674546..57674557,-p25@R3HDM2
Hg19::chr1:33360074..33360107,+p1@BC127891
Hg19::chr6:12757225..12757236,+p@chr6:12757225..12757236
+
Hg19::chr6:12955443..12955446,+p@chr6:12955443..12955446
+


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
regional part of forebrain7.79e-6641
forebrain7.79e-6641
anterior neural tube7.79e-6641
future forebrain7.79e-6641
cerebral hemisphere1.81e-6432
brain grey matter9.76e-6134
gray matter9.76e-6134
telencephalon1.65e-6034
regional part of nervous system5.97e-5953
regional part of brain5.97e-5953
regional part of telencephalon1.42e-5832
neural tube1.52e-5556
neural rod1.52e-5556
future spinal cord1.52e-5556
neural keel1.52e-5556
brain7.29e-4868
future brain7.29e-4868
nervous system8.15e-4489
pre-chordal neural plate7.68e-4361
central nervous system1.26e-4281
neural plate2.51e-3682
presumptive neural plate2.51e-3682
cerebral cortex8.45e-3625
pallium8.45e-3625
regional part of cerebral cortex2.56e-3522
neurectoderm2.18e-3486
neocortex4.99e-3320
basal ganglion2.38e-289
nuclear complex of neuraxis2.38e-289
aggregate regional part of brain2.38e-289
collection of basal ganglia2.38e-289
cerebral subcortex2.38e-289
neural nucleus4.35e-289
nucleus of brain4.35e-289
ecto-epithelium1.70e-27104
telencephalic nucleus4.27e-277
adult organism8.99e-23114
structure with developmental contribution from neural crest2.21e-22132
corpus striatum1.16e-214
striatum1.16e-214
ventral part of telencephalon1.16e-214
future corpus striatum1.16e-214
gyrus2.83e-216
ectoderm-derived structure3.90e-20171
ectoderm3.90e-20171
presumptive ectoderm3.90e-20171
organ system subdivision8.92e-18223
caudate-putamen8.40e-173
dorsal striatum8.40e-173
tube8.88e-15192
temporal lobe4.56e-126
globus pallidus8.17e-122
pallidum8.17e-122
caudate nucleus9.57e-122
future caudate nucleus9.57e-122
middle temporal gyrus1.53e-112
anatomical conduit1.27e-10240
limbic system4.02e-105
parietal lobe6.74e-105
organ part4.56e-09218
frontal cortex5.54e-083
anatomical cluster5.84e-08373
epithelium8.29e-08306
cell layer1.13e-07309
diencephalon2.51e-077
future diencephalon2.51e-077
multi-tissue structure4.96e-07342
putamen9.30e-071


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)
MA0003.10.0938548
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.10.824639
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.10.393285
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.100363
MA0074.10.819248
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.10.182167
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.11.6149
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.10.195821
MA0146.10.061409
MA0147.10.46175
MA0148.10.739888
MA0149.10.769072
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.20.928035
MA0002.20.379056
MA0137.20.558189
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.577908
MA0150.10.633493
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.10.180766
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.918944
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.00910927
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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.