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{{Coexpression_clusters
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|full_id=C3012_cerebellum_medulla_amygdala_hippocampus_occipital_middle_parietal
|id=C3012
}}

Latest revision as of 12:17, 17 September 2013


Full id: C3012_cerebellum_medulla_amygdala_hippocampus_occipital_middle_parietal



Phase1 CAGE Peaks

Hg19::chr10:3146868..3146929,+p3@PFKP
Hg19::chr17:42852832..42852834,+p@chr17:42852832..42852834
+
Hg19::chr2:39892216..39892229,+p17@TMEM178


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:00059456-phosphofructokinase complex0.0324059715622019
GO:00038726-phosphofructokinase activity0.0324059715622019
GO:0008443phosphofructokinase activity0.0324059715622019
GO:0019200carbohydrate kinase activity0.0391192555970231
GO:0005923tight junction0.0391192555970231
GO:0043296apical junction complex0.0391192555970231
GO:0016327apicolateral plasma membrane0.0391192555970231
GO:0006096glycolysis0.0391192555970231
GO:0006007glucose catabolic process0.0391192555970231
GO:0019320hexose catabolic process0.0391192555970231
GO:0046365monosaccharide catabolic process0.0391192555970231
GO:0046164alcohol catabolic process0.0391192555970231
GO:0005911intercellular junction0.0391192555970231
GO:0044275cellular carbohydrate catabolic process0.0391192555970231
GO:0044445cytosolic part0.0391192555970231
GO:0016052carbohydrate catabolic process0.0391192555970231
GO:0006006glucose metabolic process0.0391192555970231
GO:0019318hexose metabolic process0.0498895153906516
GO:0005996monosaccharide metabolic process0.0498895153906516



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 tube2.52e-9556
neural rod2.52e-9556
future spinal cord2.52e-9556
neural keel2.52e-9556
regional part of nervous system4.91e-8953
regional part of brain4.91e-8953
brain1.54e-7168
future brain1.54e-7168
central nervous system3.40e-6781
regional part of forebrain4.39e-6541
forebrain4.39e-6541
anterior neural tube4.39e-6541
future forebrain4.39e-6541
neural plate3.45e-6382
presumptive neural plate3.45e-6382
brain grey matter3.32e-6134
gray matter3.32e-6134
telencephalon5.20e-6134
neurectoderm6.00e-6086
nervous system6.73e-6089
cerebral hemisphere2.56e-5932
adult organism9.93e-56114
regional part of telencephalon9.61e-5432
regional part of cerebral cortex8.89e-5122
neocortex6.49e-4920
ecto-epithelium2.05e-48104
cerebral cortex1.74e-4425
pallium1.74e-4425
pre-chordal neural plate3.29e-4261
structure with developmental contribution from neural crest3.40e-39132
posterior neural tube4.28e-3015
chordal neural plate4.28e-3015
gyrus5.74e-296
ectoderm-derived structure3.80e-28171
ectoderm3.80e-28171
presumptive ectoderm3.80e-28171
brainstem2.10e-276
segmental subdivision of hindbrain3.10e-2412
hindbrain3.10e-2412
presumptive hindbrain3.10e-2412
tube5.81e-23192
organ system subdivision9.64e-23223
segmental subdivision of nervous system2.83e-2213
neural nucleus8.35e-189
nucleus of brain8.35e-189
anatomical conduit6.68e-17240
parietal lobe7.47e-165
frontal cortex1.57e-153
medulla oblongata7.29e-153
myelencephalon7.29e-153
future myelencephalon7.29e-153
pons2.58e-143
regional part of metencephalon3.69e-139
metencephalon3.69e-139
future metencephalon3.69e-139
organ part5.96e-13218
basal ganglion8.55e-139
nuclear complex of neuraxis8.55e-139
aggregate regional part of brain8.55e-139
collection of basal ganglia8.55e-139
cerebral subcortex8.55e-139
epithelium1.28e-12306
cell layer2.01e-12309
temporal lobe1.35e-116
anatomical cluster1.96e-11373
multi-tissue structure2.92e-11342
middle frontal gyrus4.43e-112
middle temporal gyrus5.13e-112
corpus striatum6.34e-114
striatum6.34e-114
ventral part of telencephalon6.34e-114
future corpus striatum6.34e-114
telencephalic nucleus1.18e-107
locus ceruleus3.50e-102
brainstem nucleus3.50e-102
hindbrain nucleus3.50e-102
limbic system1.89e-095
occipital lobe4.15e-095
spinal cord1.69e-073
dorsal region element1.69e-073
dorsum1.69e-073
organ4.95e-07503
caudate-putamen5.55e-073
dorsal striatum5.55e-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)
MA0003.10.178364
MA0004.10.826076
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.377374
MA0017.10.686276
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
MA0048.10.341392
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.557638
MA0056.10
MA0057.10.333427
MA0058.10.716037
MA0059.10.714521
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
MA0073.11.36698
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.715722
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
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.11.80901
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
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.10.531867
MA0145.10.273764
MA0146.10.107247
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.8915
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.20.481578
MA0102.21.88331
MA0258.10.519674
MA0259.10.575594
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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