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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:25, 17 September 2013


Full id: C550_hippocampus_amygdala_globus_medial_occipital_thalamus_middle



Phase1 CAGE Peaks

Hg19::chr3:58551312..58551323,-p@chr3:58551312..58551323
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Hg19::chr3:58551381..58551392,-p@chr3:58551381..58551392
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Hg19::chr3:58551652..58551663,-p@chr3:58551652..58551663
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Hg19::chr3:58551759..58551769,-p@chr3:58551759..58551769
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Hg19::chr3:58551789..58551800,-p@chr3:58551789..58551800
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Hg19::chr3:58552053..58552068,-p@chr3:58552053..58552068
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Hg19::chr3:58552082..58552096,-p@chr3:58552082..58552096
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Hg19::chr3:58552139..58552144,-p@chr3:58552139..58552144
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Hg19::chr3:58552163..58552174,-p@chr3:58552163..58552174
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Hg19::chr3:58552313..58552322,-p@chr3:58552313..58552322
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Hg19::chr3:58553081..58553093,-p@chr3:58553081..58553093
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Hg19::chr3:58563295..58563305,-p10@FAM107A
Hg19::chr3:58613256..58613263,-p18@FAM107A
Hg19::chr3:58613294..58613306,-p7@FAM107A
Hg19::chr3:58613323..58613342,-p4@FAM107A
Hg19::chr4:83601902..83601920,-p4@SCD5
Hg19::chr7:139416168..139416220,-p@chr7:139416168..139416220
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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:0004768stearoyl-CoA 9-desaturase activity0.0141286590560376
GO:0016717oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water0.0211904930526434



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
adult organism1.47e-80114
neural tube1.49e-7656
neural rod1.49e-7656
future spinal cord1.49e-7656
neural keel1.49e-7656
regional part of nervous system2.37e-6953
regional part of brain2.37e-6953
central nervous system6.49e-6381
neural plate1.52e-5982
presumptive neural plate1.52e-5982
nervous system2.94e-5889
brain3.66e-5768
future brain3.66e-5768
neurectoderm3.25e-5686
regional part of forebrain8.86e-5341
forebrain8.86e-5341
anterior neural tube8.86e-5341
future forebrain8.86e-5341
telencephalon7.44e-5234
brain grey matter7.92e-5234
gray matter7.92e-5234
regional part of telencephalon3.33e-4732
cerebral hemisphere6.01e-4732
ecto-epithelium2.25e-44104
structure with developmental contribution from neural crest4.47e-41132
pre-chordal neural plate7.89e-3861
regional part of cerebral cortex1.31e-3522
ectoderm-derived structure2.09e-34171
ectoderm2.09e-34171
presumptive ectoderm2.09e-34171
cerebral cortex2.64e-3425
pallium2.64e-3425
neocortex1.12e-3020
organ system subdivision1.60e-26223
posterior neural tube5.37e-2415
chordal neural plate5.37e-2415
tube1.19e-21192
basal ganglion8.30e-209
nuclear complex of neuraxis8.30e-209
aggregate regional part of brain8.30e-209
collection of basal ganglia8.30e-209
cerebral subcortex8.30e-209
anatomical conduit1.69e-19240
segmental subdivision of nervous system1.99e-1913
neural nucleus3.52e-199
nucleus of brain3.52e-199
anatomical cluster1.64e-18373
segmental subdivision of hindbrain4.27e-1712
hindbrain4.27e-1712
presumptive hindbrain4.27e-1712
brainstem9.55e-166
limbic system1.06e-145
telencephalic nucleus1.63e-147
organ part3.09e-14218
multi-tissue structure1.25e-13342
gyrus4.91e-126
corpus striatum1.17e-114
striatum1.17e-114
ventral part of telencephalon1.17e-114
future corpus striatum1.17e-114
epithelium5.12e-11306
organ8.40e-11503
cell layer8.67e-11309
temporal lobe1.39e-106
regional part of metencephalon1.49e-109
metencephalon1.49e-109
future metencephalon1.49e-109
caudate-putamen2.75e-093
dorsal striatum2.75e-093
parietal lobe4.37e-095
occipital lobe4.37e-095
spinal cord5.29e-093
dorsal region element5.29e-093
dorsum5.29e-093
medulla oblongata6.56e-093
myelencephalon6.56e-093
future myelencephalon6.56e-093
pons1.57e-083
anatomical system3.77e-07624
amygdala4.11e-072
anatomical group4.12e-07625
middle temporal gyrus4.23e-072
germ layer5.25e-07560
germ layer / neural crest5.25e-07560
embryonic tissue5.25e-07560
presumptive structure5.25e-07560
germ layer / neural crest derived structure5.25e-07560
epiblast (generic)5.25e-07560
Ammon's horn6.87e-072
lobe parts of cerebral cortex6.87e-072
hippocampal formation6.87e-072
limbic lobe6.87e-072
dorsal plus ventral thalamus7.27e-072
thalamic complex7.27e-072
embryonic structure7.59e-07564
embryo9.11e-07592


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)
MA0003.11.40118
MA0004.10.221943
MA0006.10.112549
MA0007.10.208008
MA0009.10.621697
MA0014.10.00547893
MA0017.10.137108
MA0019.10.340029
MA0024.10.525161
MA0025.10.747404
MA0027.12.20546
MA0028.10.122394
MA0029.10.542771
MA0030.10.532314
MA0031.10.474026
MA0038.10.817744
MA0040.10.548121
MA0041.10.236024
MA0042.10.608306
MA0043.10.621991
MA0046.10.611559
MA0048.10.0140676
MA0050.10.212584
MA0051.10.299199
MA0052.10.551663
MA0055.10.274153
MA0056.10
MA0057.10.327175
MA0058.10.153757
MA0059.10.15289
MA0060.10.0509127
MA0061.11.90283
MA0063.10
MA0066.10.302992
MA0067.10.924196
MA0068.10.111262
MA0069.10.607975
MA0070.10.597583
MA0071.10.27142
MA0072.10.593415
MA0073.10.0135515
MA0074.10.298586
MA0076.10.164578
MA0077.10.586275
MA0078.10.382364
MA0081.10.152999
MA0083.10.628701
MA0084.11.10674
MA0087.10.591148
MA0088.10.514158
MA0089.10
MA0090.10.518617
MA0091.10.636604
MA0092.10.195947
MA0093.10.114388
MA0095.10
MA0098.10
MA0100.10.314026
MA0101.10.749201
MA0103.10.706501
MA0105.10.288112
MA0106.10.33677
MA0107.11.40171
MA0108.20.471286
MA0109.10
MA0111.10.541878
MA0113.10.350573
MA0114.10.25223
MA0115.10.850405
MA0116.10.949722
MA0117.10.656858
MA0119.11.39041
MA0122.10.681203
MA0124.10.810546
MA0125.10.730403
MA0130.10
MA0131.10.398042
MA0132.10
MA0133.10
MA0135.10.650071
MA0136.10.30842
MA0139.10.140313
MA0140.10.269307
MA0141.11.44802
MA0142.10.445733
MA0143.10.350722
MA0144.12.37653
MA0145.10.365524
MA0146.13.20403
MA0147.10.0784275
MA0148.10.240905
MA0149.10.261654
MA0062.20.0377014
MA0035.20.268747
MA0039.20.0350337
MA0138.20.38342
MA0002.20.69807
MA0137.21.29199
MA0104.20.0505812
MA0047.20.326636
MA0112.21.0853
MA0065.20.593175
MA0150.10.170499
MA0151.10
MA0152.10.753898
MA0153.10.714423
MA0154.13.78665
MA0155.10.0782503
MA0156.10.12788
MA0157.10.421609
MA0158.10
MA0159.10.0787617
MA0160.10.703717
MA0161.10
MA0162.10.0130334
MA0163.11.48316
MA0164.10.948242
MA0080.20.11444
MA0018.20.337929
MA0099.20.27482
MA0079.20.0077743
MA0102.21.14323
MA0258.10.218609
MA0259.10.0828875
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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