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{{Coexpression_clusters
{
|full_id=C624_pituitary_cerebellum_occipital_parietal_middle_medial_hippocampus
 

Latest revision as of 11:27, 17 September 2013


Full id: C624_pituitary_cerebellum_occipital_parietal_middle_medial_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:117996926..117996946,-p@chr12:117996926..117996946
-
Hg19::chr12:118406727..118406753,-p2@KSR2
Hg19::chr12:118406887..118406903,-p8@KSR2
Hg19::chr12:118406915..118406926,-p9@KSR2
Hg19::chr12:118406929..118406949,-p4@KSR2
Hg19::chr12:130924535..130924559,-p@chr12:130924535..130924559
-
Hg19::chr13:108333449..108333463,-p@chr13:108333449..108333463
-
Hg19::chr14:93897199..93897215,+p7@UNC79
Hg19::chr17:3794021..3794042,-p4@CAMKK1
Hg19::chr1:50489500..50489513,-p4@AGBL4
Hg19::chr1:50489522..50489544,-p3@AGBL4
Hg19::chr1:50489547..50489616,-p1@AGBL4
Hg19::chr7:19813192..19813256,-p1@TMEM196
Hg19::chrX:139791917..139791938,+p1@RP1-177G6.2


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:0004674protein serine/threonine kinase activity0.0255729724364849
GO:0004683calmodulin-dependent protein kinase activity0.0255729724364849
GO:0004672protein kinase activity0.0255729724364849
GO:0006468protein amino acid phosphorylation0.0255729724364849
GO:0004182carboxypeptidase A activity0.0255729724364849
GO:0004181metallocarboxypeptidase activity0.0255729724364849
GO:0044267cellular protein metabolic process0.0255729724364849
GO:0044260cellular macromolecule metabolic process0.0255729724364849
GO:0016310phosphorylation0.0255729724364849
GO:0016773phosphotransferase activity, alcohol group as acceptor0.0255729724364849
GO:0019538protein metabolic process0.0255729724364849
GO:0019992diacylglycerol binding0.0255729724364849
GO:0004180carboxypeptidase activity0.0266709895222861
GO:0006793phosphorus metabolic process0.0266709895222861
GO:0006796phosphate metabolic process0.0266709895222861
GO:0016301kinase activity0.0266709895222861
GO:0016772transferase activity, transferring phosphorus-containing groups0.0331628902417336
GO:0008235metalloexopeptidase activity0.0331628902417336
GO:0005737cytoplasm0.0331628902417336
GO:0005516calmodulin binding0.0348677178207337
GO:0043687post-translational protein modification0.0348677178207337
GO:0008238exopeptidase activity0.0440444315224427
GO:0006464protein modification process0.0441479240308551
GO:0005524ATP binding0.0441479240308551
GO:0043412biopolymer modification0.0441479240308551
GO:0032559adenyl ribonucleotide binding0.0441479240308551
GO:0030554adenyl nucleotide binding0.0461000830774222



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
neural tube8.03e-8956
neural rod8.03e-8956
future spinal cord8.03e-8956
neural keel8.03e-8956
regional part of nervous system6.74e-8353
regional part of brain6.74e-8353
regional part of forebrain1.31e-7341
forebrain1.31e-7341
anterior neural tube1.31e-7341
future forebrain1.31e-7341
central nervous system1.12e-7281
brain7.85e-7068
future brain7.85e-7068
nervous system4.27e-6989
adult organism2.26e-64114
neural plate2.57e-6182
presumptive neural plate2.57e-6182
neurectoderm3.85e-6086
brain grey matter4.94e-5934
gray matter4.94e-5934
telencephalon5.47e-5934
cerebral hemisphere1.71e-5532
regional part of telencephalon6.13e-5532
pre-chordal neural plate3.85e-5161
ecto-epithelium1.63e-49104
regional part of cerebral cortex3.83e-4722
neocortex1.21e-4220
cerebral cortex7.06e-4125
pallium7.06e-4125
structure with developmental contribution from neural crest5.53e-39132
ectoderm-derived structure1.42e-35171
ectoderm1.42e-35171
presumptive ectoderm1.42e-35171
organ system subdivision6.38e-30223
tube5.51e-20192
basal ganglion8.82e-209
nuclear complex of neuraxis8.82e-209
aggregate regional part of brain8.82e-209
collection of basal ganglia8.82e-209
cerebral subcortex8.82e-209
neural nucleus1.92e-199
nucleus of brain1.92e-199
anatomical conduit4.28e-17240
anatomical cluster1.84e-16373
posterior neural tube2.68e-1615
chordal neural plate2.68e-1615
diencephalon1.08e-157
future diencephalon1.08e-157
telencephalic nucleus1.77e-157
gyrus6.74e-156
brainstem2.18e-136
epithelium8.21e-13306
limbic system1.24e-125
cell layer1.55e-12309
parietal lobe1.64e-125
occipital lobe2.99e-125
temporal lobe3.01e-126
organ part4.16e-12218
multi-tissue structure1.80e-11342
segmental subdivision of hindbrain2.84e-1112
hindbrain2.84e-1112
presumptive hindbrain2.84e-1112
corpus striatum2.70e-104
striatum2.70e-104
ventral part of telencephalon2.70e-104
future corpus striatum2.70e-104
segmental subdivision of nervous system2.77e-1013
gland of diencephalon2.83e-104
neuroendocrine gland2.83e-104
organ4.56e-10503
embryo8.79e-10592
regional part of diencephalon2.70e-094
frontal cortex1.72e-083
developing anatomical structure3.99e-08581
germ layer4.10e-08560
germ layer / neural crest4.10e-08560
embryonic tissue4.10e-08560
presumptive structure4.10e-08560
germ layer / neural crest derived structure4.10e-08560
epiblast (generic)4.10e-08560
caudate-putamen4.43e-083
dorsal striatum4.43e-083
embryonic structure6.41e-08564
pons1.13e-073
medulla oblongata2.22e-073
myelencephalon2.22e-073
future myelencephalon2.22e-073
multi-cellular organism2.58e-07656
spinal cord3.59e-073
dorsal region element3.59e-073
dorsum3.59e-073
male genital duct7.44e-073
internal male genitalia7.44e-073


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)
MA0003.12.189
MA0004.10.275994
MA0006.11.45329
MA0007.10.260673
MA0009.10.695988
MA0014.13.67447
MA0017.10.534321
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.953078
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.12.05724
MA0050.10.265714
MA0051.10.359609
MA0052.10.623986
MA0055.11.58506
MA0056.10
MA0057.11.12385
MA0058.10.200063
MA0059.10.199079
MA0060.10.0773489
MA0061.10.224865
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.13.15269
MA0069.10.681911
MA0070.15.26679
MA0071.10.329767
MA0072.10.666958
MA0073.12.01629
MA0074.10.358953
MA0076.10.609177
MA0077.10.65962
MA0078.10.447828
MA0081.10.199203
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.11.06443
MA0089.10
MA0090.10.223576
MA0091.10.762163
MA0092.10.247341
MA0093.10.154754
MA0095.10
MA0098.10
MA0100.11.74006
MA0101.10.92504
MA0103.10.146091
MA0105.10.0899037
MA0106.17.15279
MA0107.10.708233
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.10.414278
MA0114.11.14609
MA0115.10.929032
MA0116.10.354243
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.453946
MA0140.10.327488
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.0953756
MA0145.10.324645
MA0146.12.56474
MA0147.10.36013
MA0148.10.296708
MA0149.11.5426
MA0062.20.0599644
MA0035.20.326883
MA0039.21.04569
MA0138.21.13988
MA0002.20.248488
MA0137.20.168782
MA0104.20.265556
MA0047.20.388882
MA0112.20.0113102
MA0065.20.333967
MA0150.10.218956
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.687815
MA0155.11.05452
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.112236
MA0160.10.30953
MA0161.10
MA0162.14.46014
MA0163.10.317359
MA0164.10.425415
MA0080.20.154815
MA0018.20.400879
MA0099.20.333432
MA0079.27.2706
MA0102.21.22472
MA0258.10.089643
MA0259.10.374338
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
E2F1#186972.453694607439660.01287341320003250.0463120940097894
PBX3#509046.261289339069750.002998943887654680.0159392722993775
YY1#752872.455585374926930.01281875463892510.0461186370779117
ZBTB33#1000936.785298220710250.008823699110461790.0335068287604086
ZEB1#693544.825266290726820.007607370633686160.031350123569094



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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