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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,

Latest revision as of 11:24, 17 September 2013


Full id: C499_medulla_thalamus_spinal_globus_optic_caudate_hippocampus



Phase1 CAGE Peaks

Hg19::chr12:41365353..41365362,+p@chr12:41365353..41365362
+
Hg19::chr15:59664884..59664903,+p4@FAM81A
Hg19::chr17:42991223..42991232,-p@chr17:42991223..42991232
-
Hg19::chr18:24434129..24434169,-p8@AQP4
Hg19::chr18:24434187..24434198,-p13@AQP4
Hg19::chr18:24435190..24435201,-p@chr18:24435190..24435201
-
Hg19::chr18:74691180..74691220,-p@chr18:74691180..74691220
-
Hg19::chr18:74691599..74691602,+p@chr18:74691599..74691602
+
Hg19::chr1:204991565..204991578,+p@chr1:204991565..204991578
+
Hg19::chr1:68849935..68849943,-p@chr1:68849935..68849943
-
Hg19::chr1:85786236..85786252,-p30@DDAH1
Hg19::chr6:164348089..164348100,+p@chr6:164348089..164348100
+
Hg19::chr8:26491964..26491967,+p@chr8:26491964..26491967
+
Hg19::chr8:28965684..28965712,-p4@KIF13B
Hg19::chr9:87426149..87426182,+p25@NTRK2
Hg19::chr9:87426979..87426990,+p54@NTRK2
Hg19::chr9:87427842..87427853,+p46@NTRK2
Hg19::chr9:87429337..87429348,+p57@NTRK2
Hg19::chrX:13792037..13792048,-p@chrX:13792037..13792048
-


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:0016403dimethylargininase activity0.0259898459425752
GO:0043121neurotrophin binding0.0259898459425752
GO:0007263nitric oxide mediated signal transduction0.0259898459425752
GO:0006527arginine catabolic process0.0259898459425752
GO:0015250water channel activity0.0259898459425752
GO:0005372water transporter activity0.0297760869891295
GO:0009065glutamine family amino acid catabolic process0.0396763042251676
GO:0016813hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines0.0396763042251676
GO:0007399nervous system development0.0396763042251676
GO:0006525arginine metabolic process0.040578659960201
GO:0000051urea cycle intermediate metabolic process0.0472042095940519



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 tube1.15e-12856
neural rod1.15e-12856
future spinal cord1.15e-12856
neural keel1.15e-12856
regional part of nervous system3.04e-11753
regional part of brain3.04e-11753
regional part of forebrain2.42e-9841
forebrain2.42e-9841
anterior neural tube2.42e-9841
future forebrain2.42e-9841
central nervous system4.49e-9881
brain1.37e-9768
future brain1.37e-9768
nervous system1.02e-9189
neural plate1.11e-8982
presumptive neural plate1.11e-8982
brain grey matter2.43e-8634
gray matter2.43e-8634
telencephalon1.57e-8534
neurectoderm4.15e-8586
regional part of telencephalon9.27e-7932
cerebral hemisphere2.04e-7832
ecto-epithelium7.77e-69104
pre-chordal neural plate3.00e-6861
adult organism1.11e-65114
regional part of cerebral cortex9.35e-6222
structure with developmental contribution from neural crest1.58e-57132
neocortex3.29e-5420
cerebral cortex4.83e-5425
pallium4.83e-5425
ectoderm-derived structure9.15e-44171
ectoderm9.15e-44171
presumptive ectoderm9.15e-44171
neural nucleus1.36e-349
nucleus of brain1.36e-349
basal ganglion2.54e-349
nuclear complex of neuraxis2.54e-349
aggregate regional part of brain2.54e-349
collection of basal ganglia2.54e-349
cerebral subcortex2.54e-349
organ system subdivision7.82e-33223
tube4.18e-31192
posterior neural tube1.52e-2915
chordal neural plate1.52e-2915
telencephalic nucleus5.90e-277
brainstem2.26e-236
anatomical conduit6.14e-23240
segmental subdivision of nervous system8.89e-2313
gyrus5.40e-226
limbic system5.20e-205
segmental subdivision of hindbrain1.84e-1912
hindbrain1.84e-1912
presumptive hindbrain1.84e-1912
occipital lobe5.68e-195
epithelium4.88e-18306
cell layer9.14e-18309
anatomical cluster1.27e-16373
regional part of diencephalon4.87e-164
corpus striatum7.74e-164
striatum7.74e-164
ventral part of telencephalon7.74e-164
future corpus striatum7.74e-164
organ part1.78e-15218
diencephalon7.07e-147
future diencephalon7.07e-147
temporal lobe1.43e-136
spinal cord5.14e-133
dorsal region element5.14e-133
dorsum5.14e-133
multi-tissue structure5.35e-13342
medulla oblongata1.23e-123
myelencephalon1.23e-123
future myelencephalon1.23e-123
caudate-putamen1.43e-123
dorsal striatum1.43e-123
pons1.74e-123
parietal lobe2.62e-125
frontal cortex3.24e-123
regional part of metencephalon2.02e-109
metencephalon2.02e-109
future metencephalon2.02e-109
Ammon's horn2.20e-092
lobe parts of cerebral cortex2.20e-092
hippocampal formation2.20e-092
limbic lobe2.20e-092
locus ceruleus2.29e-092
brainstem nucleus2.29e-092
hindbrain nucleus2.29e-092
dorsal plus ventral thalamus2.39e-092
globus pallidus2.39e-092
pallidum2.39e-092
thalamic complex2.39e-092
amygdala4.36e-092
caudate nucleus4.36e-092
future caudate nucleus4.36e-092
multi cell component structure4.53e-092
neuron projection bundle4.53e-092
middle frontal gyrus6.73e-092
organ6.76e-09503
middle temporal gyrus1.58e-082


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)
MA0003.12.8722e-05
MA0004.10.193314
MA0006.10.0925234
MA0007.10.532323
MA0009.11.41914
MA0014.10.00883981
MA0017.10.367718
MA0019.10.305657
MA0024.10.485346
MA0025.10.70396
MA0027.12.15732
MA0028.10.101383
MA0029.10.50258
MA0030.10.492344
MA0031.10.435419
MA0038.11.36368
MA0040.10.507819
MA0041.10.206566
MA0042.10.183918
MA0043.10.580321
MA0046.11.39813
MA0048.10.131175
MA0050.11.03704
MA0051.10.266537
MA0052.10.511289
MA0055.10.0183725
MA0056.10
MA0057.10.122328
MA0058.10.407083
MA0059.10.405044
MA0060.10.0387582
MA0061.10.029485
MA0063.10
MA0066.10.743889
MA0067.10.879057
MA0068.10.671958
MA0069.10.566544
MA0070.10.556335
MA0071.10.674412
MA0072.10.552241
MA0073.10.438849
MA0074.10.734236
MA0076.10.139892
MA0077.10.545231
MA0078.10.346453
MA0081.10.129245
MA0083.11.43365
MA0084.11.06048
MA0087.10.550016
MA0088.10.0166254
MA0089.10
MA0090.10.891785
MA0091.11.07936
MA0092.11.54999
MA0093.10.313082
MA0095.10
MA0098.10
MA0100.10.768006
MA0101.10.0959778
MA0103.10.614572
MA0105.10.00666152
MA0106.10.302526
MA0107.10.46886
MA0108.20.432749
MA0109.10
MA0111.10.15804
MA0113.10.847356
MA0114.10.456488
MA0115.10.805883
MA0116.10.0607301
MA0117.10.614633
MA0119.10.379868
MA0122.10.638621
MA0124.10.766407
MA0125.10.687166
MA0130.10
MA0131.10.361613
MA0132.10
MA0133.10
MA0135.10.60795
MA0136.12.12534
MA0139.10.0257123
MA0140.10.669735
MA0141.10.402298
MA0142.11.05085
MA0143.10.315941
MA0144.10.741474
MA0145.10.278749
MA0146.10.000305288
MA0147.10.223797
MA0148.11.7874
MA0149.10.230803
MA0062.20.027823
MA0035.20.668495
MA0039.20.0161404
MA0138.20.347473
MA0002.20.138689
MA0137.20.105044
MA0104.20.151208
MA0047.20.292798
MA0112.20.136364
MA0065.20.156004
MA0150.10.145358
MA0151.10
MA0152.10.681299
MA0153.10.67139
MA0154.10.214105
MA0155.10.236629
MA0156.10.703429
MA0157.10.99963
MA0158.10
MA0159.10.840681
MA0160.10.632864
MA0161.10
MA0162.10.00153143
MA0163.10.0567345
MA0164.10.870085
MA0080.21.59109
MA0018.20.30364
MA0099.20.681929
MA0079.25.95052e-06
MA0102.21.09681
MA0258.10.399676
MA0259.10.235101
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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