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{{Coexpression_clusters
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|full_id=C2972_brain_pineal_temporal_parietal_occipital_duodenum_putamen
|id=C2972
}}

Latest revision as of 12:16, 17 September 2013


Full id: C2972_brain_pineal_temporal_parietal_occipital_duodenum_putamen



Phase1 CAGE Peaks

Hg19::chr10:104178483..104178500,-p5@PSD
Hg19::chr10:104178506..104178574,-p2@PSD
Hg19::chr11:107461940..107461945,+p6@ELMOD1


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:0005086ARF guanyl-nucleotide exchange factor activity0.0434219658401055
GO:0006909phagocytosis0.0434219658401055
GO:0032011ARF protein signal transduction0.0439243163135562
GO:0032012regulation of ARF protein signal transduction0.0439243163135562



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
embryonic stem cell7.69e-105
neuronal stem cell7.22e-098
neuron2.28e-086
neuroblast2.28e-086
electrically signaling cell2.28e-086
neural cell5.06e-0725
Uber Anatomy
Ontology termp-valuen
central nervous system4.10e-8881
nervous system2.75e-8689
neural tube2.17e-8156
neural rod2.17e-8156
future spinal cord2.17e-8156
neural keel2.17e-8156
regional part of nervous system8.93e-7653
regional part of brain8.93e-7653
brain1.27e-7068
future brain1.27e-7068
regional part of forebrain4.91e-6841
forebrain4.91e-6841
anterior neural tube4.91e-6841
future forebrain4.91e-6841
neurectoderm5.28e-6086
neural plate1.07e-5882
presumptive neural plate1.07e-5882
cerebral hemisphere7.03e-5832
brain grey matter1.64e-5734
gray matter1.64e-5734
telencephalon1.81e-5734
regional part of telencephalon8.42e-5432
pre-chordal neural plate5.58e-5061
ecto-epithelium4.38e-47104
ectoderm-derived structure2.86e-46171
ectoderm2.86e-46171
presumptive ectoderm2.86e-46171
regional part of cerebral cortex5.56e-4622
cerebral cortex2.74e-4325
pallium2.74e-4325
neocortex1.57e-4120
structure with developmental contribution from neural crest1.45e-35132
organ system subdivision9.56e-33223
adult organism1.15e-31114
temporal lobe1.41e-166
basal ganglion3.78e-169
nuclear complex of neuraxis3.78e-169
aggregate regional part of brain3.78e-169
collection of basal ganglia3.78e-169
cerebral subcortex3.78e-169
tube6.51e-16192
neural nucleus2.39e-159
nucleus of brain2.39e-159
posterior neural tube1.21e-1415
chordal neural plate1.21e-1415
anatomical cluster1.92e-14373
gyrus4.24e-146
limbic system1.01e-125
brainstem4.27e-126
parietal lobe4.29e-125
telencephalic nucleus8.33e-127
diencephalon1.19e-117
future diencephalon1.19e-117
anatomical conduit8.54e-11240
corpus striatum2.96e-104
striatum2.96e-104
ventral part of telencephalon2.96e-104
future corpus striatum2.96e-104
gland of diencephalon4.28e-104
neuroendocrine gland4.28e-104
segmental subdivision of hindbrain6.08e-1012
hindbrain6.08e-1012
presumptive hindbrain6.08e-1012
organ part1.70e-09218
segmental subdivision of nervous system4.55e-0913
epithelium6.31e-09306
cell layer1.04e-08309
caudate-putamen4.53e-083
dorsal striatum4.53e-083
occipital lobe5.04e-085
frontal cortex7.18e-083
embryo1.19e-07592
pons5.58e-073
spinal cord6.47e-073
dorsal region element6.47e-073
dorsum6.47e-073
medulla oblongata9.25e-073
myelencephalon9.25e-073
future myelencephalon9.25e-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)
MA0003.10.708947
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
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
MA0048.11.62115
MA0050.10.81185
MA0051.10.936307
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.11.84332
MA0069.11.31207
MA0070.11.30033
MA0071.10.897953
MA0072.11.29561
MA0073.18.0808
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
MA0093.11.55117
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
MA0111.10.767139
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
MA0145.10.752137
MA0146.10.707589
MA0147.10.565108
MA0148.10.854239
MA0149.10.884158
MA0062.21.141
MA0035.20.894194
MA0039.23.37171
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.20.491226
MA0047.20.973066
MA0112.20.731309
MA0065.20.760954
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.838867
MA0155.12.02721
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.11.38935
MA0160.10.871361
MA0161.10
MA0162.12.05956
MA0163.10.776149
MA0164.11.01792
MA0080.20.643061
MA0018.20.987913
MA0099.20.902716
MA0079.27.52072
MA0102.21.88331
MA0258.11.29138
MA0259.11.40979
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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