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{{Coexpression_clusters
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|full_id=C1379_pineal_cerebellum_small_occipital_parietal_temporal_hippocampus
|id=C1379
}}

Latest revision as of 11:43, 17 September 2013


Full id: C1379_pineal_cerebellum_small_occipital_parietal_temporal_hippocampus



Phase1 CAGE Peaks

Hg19::chr13:25745685..25745777,-p1@FAM123A
Hg19::chr15:51973635..51973646,+p4@SCG3
Hg19::chr19:42470940..42470980,-p@chr19:42470940..42470980
-
Hg19::chr5:11903337..11903377,-p18@CTNND2
Hg19::chr6:127837142..127837208,-p1@C6orf174
Hg19::chr6:25279289..25279415,+p3@LRRC16A


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:0007158neuron adhesion0.0296662538128231



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>cell_data<br>uberon_data<br><br>

Cell Type
Ontology termp-valuen
neuronal stem cell1.12e-078
Uber Anatomy
Ontology termp-valuen
nervous system2.76e-6889
central nervous system3.10e-6781
neural tube1.89e-6556
neural rod1.89e-6556
future spinal cord1.89e-6556
neural keel1.89e-6556
regional part of nervous system1.62e-6153
regional part of brain1.62e-6153
neurectoderm1.75e-5686
neural plate1.41e-5482
presumptive neural plate1.41e-5482
regional part of forebrain4.52e-5441
forebrain4.52e-5441
anterior neural tube4.52e-5441
future forebrain4.52e-5441
brain4.76e-5468
future brain4.76e-5468
adult organism1.30e-47114
brain grey matter3.45e-4534
gray matter3.45e-4534
telencephalon6.01e-4534
ecto-epithelium1.89e-44104
ectoderm-derived structure2.59e-43171
ectoderm2.59e-43171
presumptive ectoderm2.59e-43171
cerebral hemisphere1.15e-4232
regional part of telencephalon1.87e-4232
pre-chordal neural plate3.36e-4261
cerebral cortex8.78e-3425
pallium8.78e-3425
structure with developmental contribution from neural crest2.18e-33132
regional part of cerebral cortex1.59e-3122
organ system subdivision6.00e-29223
neocortex6.63e-2920
anatomical cluster3.32e-15373
tube8.49e-14192
basal ganglion1.09e-129
nuclear complex of neuraxis1.09e-129
aggregate regional part of brain1.09e-129
collection of basal ganglia1.09e-129
cerebral subcortex1.09e-129
neural nucleus1.17e-129
nucleus of brain1.17e-129
posterior neural tube1.40e-1215
chordal neural plate1.40e-1215
organ part4.85e-11218
temporal lobe2.50e-106
diencephalon2.61e-107
future diencephalon2.61e-107
segmental subdivision of nervous system3.93e-1013
telencephalic nucleus4.90e-107
anatomical conduit4.93e-10240
gyrus1.42e-096
segmental subdivision of hindbrain3.65e-0912
hindbrain3.65e-0912
presumptive hindbrain3.65e-0912
brainstem6.98e-096
occipital lobe1.85e-085
limbic system4.32e-085
parietal lobe4.84e-085
embryo1.06e-07592
multi-tissue structure1.42e-07342
epithelium4.16e-07306
organ6.51e-07503
multi-cellular organism6.99e-07656
cell layer7.33e-07309
gland of diencephalon8.45e-074
neuroendocrine gland8.45e-074
regional part of diencephalon8.82e-074


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)
MA0003.10.321379
MA0004.10.558729
MA0006.10.391183
MA0007.10.539222
MA0009.11.03681
MA0014.10.491287
MA0017.10.432438
MA0019.10.7124
MA0024.10.929647
MA0025.11.17262
MA0027.12.65688
MA0028.10.408079
MA0029.10.949428
MA0030.10.937696
MA0031.10.871496
MA0038.10.665566
MA0040.10.955415
MA0041.10.578072
MA0042.10.544748
MA0043.11.03713
MA0046.11.02569
MA0048.10.152639
MA0050.10.545671
MA0051.10.661179
MA0052.10.959373
MA0055.10.465994
MA0056.10
MA0057.10.882847
MA0058.10.458909
MA0059.10.457555
MA0060.10.267412
MA0061.11.24837
MA0063.10
MA0066.10.66601
MA0067.11.35893
MA0068.10.578694
MA0069.11.02175
MA0070.11.01032
MA0071.10.625297
MA0072.11.00572
MA0073.10.216116
MA0074.10.660398
MA0076.10.475586
MA0077.10.997832
MA0078.10.763954
MA0081.10.457725
MA0083.11.04447
MA0084.11.5477
MA0087.11.00322
MA0088.10.32124
MA0089.10
MA0090.10.490736
MA0091.11.37996
MA0092.10.522012
MA0093.10.394379
MA0095.10
MA0098.10
MA0100.10.679972
MA0101.10.397846
MA0103.10.381434
MA0105.11.34409
MA0106.10.70837
MA0107.10.857383
MA0108.20.868347
MA0109.10
MA0111.10.504913
MA0113.10.725375
MA0114.10.314898
MA0115.11.28169
MA0116.10.865577
MA0117.11.07516
MA0119.10.440684
MA0122.11.10154
MA0124.11.23968
MA0125.11.15445
MA0130.10
MA0131.10.782708
MA0132.10
MA0133.10
MA0135.11.06778
MA0136.10.672893
MA0139.10.641617
MA0140.10.622527
MA0141.10.455728
MA0142.10.838805
MA0143.10.725558
MA0144.10.299851
MA0145.10.107156
MA0146.10.441872
MA0147.10.327615
MA0148.10.584698
MA0149.10.612449
MA0062.20.23336
MA0035.20.621793
MA0039.20.35955
MA0138.20.765223
MA0002.20.709311
MA0137.20.414885
MA0104.20.26661
MA0047.20.695777
MA0112.21.65732
MA0065.20.354331
MA0150.10.484557
MA0151.10
MA0152.10.629368
MA0153.11.13732
MA0154.10.413181
MA0155.10.0961854
MA0156.10.417278
MA0157.10.810597
MA0158.10
MA0159.10.328286
MA0160.10.600559
MA0161.10
MA0162.11.39622
MA0163.10.813808
MA0164.10.738243
MA0080.20.394469
MA0018.20.709805
MA0099.20.629739
MA0079.24.76174
MA0102.21.58513
MA0258.10.788656
MA0259.10.336472
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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