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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0,0

Latest revision as of 11:29, 17 September 2013


Full id: C710_anaplastic_cerebellum_xeroderma_B_carcinoid_merkel_occipital



Phase1 CAGE Peaks

Hg19::chr3:141103404..141103414,+p74@ZBTB38
Hg19::chr3:141103437..141103451,+p55@ZBTB38
Hg19::chr3:141103589..141103603,+p34@ZBTB38
Hg19::chr3:141103634..141103665,+p18@ZBTB38
Hg19::chr7:119913185..119913236,+p1@KCND2
Hg19::chr7:119913374..119913397,+p3@KCND2
Hg19::chr7:119913850..119913858,+p5@KCND2
Hg19::chr7:119913908..119913917,+p13@KCND2
Hg19::chr7:119935318..119935329,+p@chr7:119935318..119935329
+
Hg19::chr7:119993211..119993216,+p@chr7:119993211..119993216
+
Hg19::chr7:120099066..120099074,+p@chr7:120099066..120099074
+
Hg19::chr7:120170697..120170712,+p@chr7:120170697..120170712
+


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:0043197dendritic spine0.0349674017569853



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
Merkel cell6.68e-082
Uber Anatomy
Ontology termp-valuen
regional part of nervous system4.12e-8453
regional part of brain4.12e-8453
neural tube1.54e-8356
neural rod1.54e-8356
future spinal cord1.54e-8356
neural keel1.54e-8356
regional part of forebrain2.28e-6841
forebrain2.28e-6841
anterior neural tube2.28e-6841
future forebrain2.28e-6841
central nervous system6.19e-6681
brain9.00e-6668
future brain9.00e-6668
brain grey matter1.00e-6234
gray matter1.00e-6234
nervous system2.30e-5889
telencephalon3.49e-5834
cerebral hemisphere1.36e-5732
regional part of telencephalon2.32e-5732
neural plate5.43e-5482
presumptive neural plate5.43e-5482
neurectoderm1.10e-5386
regional part of cerebral cortex1.21e-4922
neocortex1.91e-4920
ecto-epithelium2.08e-45104
pre-chordal neural plate1.75e-4361
cerebral cortex2.79e-4325
pallium2.79e-4325
adult organism6.57e-34114
structure with developmental contribution from neural crest2.16e-31132
ectoderm-derived structure3.62e-30171
ectoderm3.62e-30171
presumptive ectoderm3.62e-30171
tube6.17e-22192
organ system subdivision1.77e-21223
basal ganglion5.25e-219
nuclear complex of neuraxis5.25e-219
aggregate regional part of brain5.25e-219
collection of basal ganglia5.25e-219
cerebral subcortex5.25e-219
neural nucleus1.03e-209
nucleus of brain1.03e-209
gyrus3.61e-186
occipital lobe2.54e-165
segmental subdivision of hindbrain2.87e-1612
hindbrain2.87e-1612
presumptive hindbrain2.87e-1612
posterior neural tube4.41e-1615
chordal neural plate4.41e-1615
telencephalic nucleus2.08e-157
temporal lobe2.13e-156
anatomical conduit2.29e-15240
segmental subdivision of nervous system6.67e-1513
regional part of metencephalon5.97e-139
metencephalon5.97e-139
future metencephalon5.97e-139
brainstem6.47e-136
organ part6.52e-12218
epithelium2.40e-11306
diencephalon2.70e-117
future diencephalon2.70e-117
cell layer3.95e-11309
parietal lobe1.53e-105
limbic system1.95e-105
pons3.27e-103
frontal cortex5.92e-103
anatomical cluster1.39e-09373
corpus striatum5.77e-084
striatum5.77e-084
ventral part of telencephalon5.77e-084
future corpus striatum5.77e-084
dorsal plus ventral thalamus1.09e-072
thalamic complex1.09e-072
amygdala2.01e-072
pituitary gland2.29e-072
middle temporal gyrus2.60e-072
middle frontal gyrus4.02e-072
locus ceruleus4.42e-072
brainstem nucleus4.42e-072
hindbrain nucleus4.42e-072
multi-tissue structure4.67e-07342
globus pallidus8.65e-072
pallidum8.65e-072


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)
MA0003.10.00251029
MA0004.10.32225
MA0006.10.188769
MA0007.10.825205
MA0009.10.756202
MA0014.10.455267
MA0017.10.220105
MA0019.10.45566
MA0024.10.654931
MA0025.10.886436
MA0027.12.35633
MA0028.10.201461
MA0029.10.673506
MA0030.10.662482
MA0031.10.600685
MA0038.10.414169
MA0040.10.67914
MA0041.10.338572
MA0042.10.835565
MA0043.10.756508
MA0046.10.745626
MA0048.10.0399193
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.10.400018
MA0056.10
MA0057.10.3421
MA0058.10.240796
MA0059.10.239727
MA0060.10.103131
MA0061.10.0856761
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.8463
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.532302
MA0074.10.40963
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.397386
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.10.535462
MA0105.10.0320473
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.11.17934
MA0114.10.134281
MA0115.10.992167
MA0116.10.433848
MA0117.10.792789
MA0119.10.226505
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.10.0781324
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.10.0212759
MA0146.10.00710499
MA0147.10.143012
MA0148.10.344198
MA0149.10.367947
MA0062.20.280813
MA0035.20.376007
MA0039.20.0300713
MA0138.20.503176
MA0002.20.0954816
MA0137.20.20663
MA0104.20.102626
MA0047.21.12244
MA0112.20.0192555
MA0065.20.23889
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.0310431
MA0155.10.0793743
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.11.39808
MA0160.10.940794
MA0161.10
MA0162.11.19068
MA0163.10.0369192
MA0164.10.478818
MA0080.20.558855
MA0018.20.453345
MA0099.20.382887
MA0079.20.250032
MA0102.21.28978
MA0258.10.117513
MA0259.10.455773
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
ZEB1#693545.629477339181290.0041376490332310.0197203453375445



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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