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{{Coexpression_clusters
{
|full_id=C713_skeletal_heart_Renal_aorta_Fibroblast_Smooth_mature
|

Latest revision as of 11:29, 17 September 2013


Full id: C713_skeletal_heart_Renal_aorta_Fibroblast_Smooth_mature



Phase1 CAGE Peaks

Hg19::chr5:150004188..150004308,+p1@SYNPO
Hg19::chr5:150027636..150027663,+p2@AB384087
Hg19::chr5:150027742..150027754,+p3@AB384087
Hg19::chr5:150027815..150027828,+p1@AB384087
Hg19::chr5:150027838..150027865,+p6@SYNPO
Hg19::chr5:150027893..150027907,+p15@SYNPO
Hg19::chr5:150027978..150028011,+p13@SYNPO
Hg19::chr5:150028043..150028054,+p23@SYNPO
Hg19::chr5:150028060..150028075,+p22@SYNPO
Hg19::chr5:150028080..150028174,-p@chr5:150028080..150028174
-
Hg19::chr5:150028254..150028266,+p16@SYNPO
Hg19::chr5:150029105..150029117,+p@chr5:150029105..150029117
+


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:0043204perikaryon0.0027375485694101
GO:0043197dendritic spine0.0027375485694101
GO:0043025cell soma0.00857765218415165
GO:0030425dendrite0.00857765218415165
GO:0044463cell projection part0.00857765218415165
GO:0043005neuron projection0.0106460222143726
GO:0005923tight junction0.0106460222143726
GO:0043296apical junction complex0.0106460222143726
GO:0016327apicolateral plasma membrane0.0106460222143726
GO:0045211postsynaptic membrane0.0131554417363319
GO:0044456synapse part0.0131554417363319
GO:0005911intercellular junction0.0131554417363319
GO:0015629actin cytoskeleton0.0204012548148896
GO:0042995cell projection0.0204012548148896
GO:0030054cell junction0.0249801306958672
GO:0003779actin binding0.0249801306958672
GO:0008092cytoskeletal protein binding0.0323674860265547



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>

Uber Anatomy
Ontology termp-valuen
adult organism3.96e-30114
anatomical conduit2.84e-29240
anatomical cluster3.52e-26373
tube9.27e-25192
epithelium1.59e-17306
splanchnic layer of lateral plate mesoderm3.76e-1783
cell layer3.85e-17309
vessel1.33e-1668
vasculature1.65e-1678
vascular system1.65e-1678
epithelial tube open at both ends3.37e-1559
blood vessel3.37e-1559
blood vasculature3.37e-1559
vascular cord3.37e-1559
circulatory system4.48e-15112
structure with developmental contribution from neural crest2.18e-14132
epithelial tube2.51e-14117
multi-tissue structure2.54e-14342
cardiovascular system1.29e-13109
regional part of forebrain2.09e-1341
forebrain2.09e-1341
anterior neural tube2.09e-1341
future forebrain2.09e-1341
telencephalon4.49e-1334
cerebral hemisphere4.50e-1332
neural tube5.39e-1356
neural rod5.39e-1356
future spinal cord5.39e-1356
neural keel5.39e-1356
brain grey matter7.44e-1334
gray matter7.44e-1334
regional part of nervous system9.28e-1353
regional part of brain9.28e-1353
regional part of telencephalon1.15e-1232
neural plate3.41e-1282
presumptive neural plate3.41e-1282
brain9.86e-1268
future brain9.86e-1268
neurectoderm3.48e-1186
regional part of cerebral cortex7.60e-1122
primary circulatory organ1.66e-1027
artery5.45e-1042
arterial blood vessel5.45e-1042
arterial system5.45e-1042
cerebral cortex9.50e-1025
pallium9.50e-1025
central nervous system1.02e-0981
neocortex1.65e-0920
ecto-epithelium1.74e-09104
pre-chordal neural plate2.57e-0961
anatomical system5.90e-09624
anatomical group8.14e-09625
compound organ9.09e-0968
heart1.20e-0824
primitive heart tube1.20e-0824
primary heart field1.20e-0824
anterior lateral plate mesoderm1.20e-0824
heart tube1.20e-0824
heart primordium1.20e-0824
cardiac mesoderm1.20e-0824
cardiogenic plate1.20e-0824
heart rudiment1.20e-0824
multi-cellular organism5.94e-08656
organ system subdivision2.01e-07223
embryonic structure2.22e-07564
nervous system2.22e-0789
germ layer2.68e-07560
germ layer / neural crest2.68e-07560
embryonic tissue2.68e-07560
presumptive structure2.68e-07560
germ layer / neural crest derived structure2.68e-07560
epiblast (generic)2.68e-07560
blood vessel endothelium3.59e-0718
endothelium3.59e-0718
cardiovascular system endothelium3.59e-0718


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)
MA0003.10.0958548
MA0004.10.32225
MA0006.10.188769
MA0007.10.305951
MA0009.10.756202
MA0014.10.657865
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
MA0042.10.310552
MA0043.10.756508
MA0046.10.745626
MA0048.11.90675
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.11.58906
MA0056.10
MA0057.10.965996
MA0058.10.240796
MA0059.10.239727
MA0060.11.67287
MA0061.10.0856761
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.10.379038
MA0072.10.726666
MA0073.10.142258
MA0074.13.79118
MA0076.10.254045
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.20556
MA0089.10
MA0090.10.734839
MA0091.10.324543
MA0092.10.291716
MA0093.10.191154
MA0095.10
MA0098.10
MA0100.10.426863
MA0101.10.19375
MA0103.11.02503
MA0105.10.0320473
MA0106.10.452066
MA0107.10.137948
MA0108.20.597764
MA0109.10
MA0111.10.277713
MA0113.10.467266
MA0114.10.134281
MA0115.10.992167
MA0116.10.140463
MA0117.10.792789
MA0119.11.87032
MA0122.10.818044
MA0124.10.951337
MA0125.10.868909
MA0130.10
MA0131.10.519055
MA0132.10
MA0133.10
MA0135.10.785738
MA0136.10.420617
MA0139.11.97962
MA0140.10.376643
MA0141.11.24597
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.11.05522
MA0146.12.01134
MA0147.10.143012
MA0148.10.910784
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.20.431698
MA0138.20.503176
MA0002.20.652621
MA0137.20.20663
MA0104.20.102626
MA0047.20.440861
MA0112.20.0192555
MA0065.20.096411
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.10.126936
MA0155.10.0793743
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.10.143477
MA0160.10.357736
MA0161.10
MA0162.10.00310762
MA0163.10.00158421
MA0164.10.478818
MA0080.20.191221
MA0018.20.453345
MA0099.20.382887
MA0079.20.0700316
MA0102.21.28978
MA0258.10.375
MA0259.10.149181
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
ZNF263#1012785.481227758007121.50025403478449e-050.000355456059752399



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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