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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:28, 17 September 2013


Full id: C676_serous_CD8_CD4_Natural_gall_cerebellum_Basophils



Phase1 CAGE Peaks

Hg19::chr10:73819242..73819255,-p@chr10:73819242..73819255
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Hg19::chr10:73821340..73821373,-p@chr10:73821340..73821373
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Hg19::chr10:73822482..73822493,-p@chr10:73822482..73822493
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Hg19::chr10:73822528..73822532,-p@chr10:73822528..73822532
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Hg19::chr10:73823970..73824002,-p@chr10:73823970..73824002
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Hg19::chr10:73848088..73848099,-p9@SPOCK2
Hg19::chr10:73848196..73848207,-p6@SPOCK2
Hg19::chr10:73848209..73848220,-p7@SPOCK2
Hg19::chr10:73848236..73848250,-p2@SPOCK2
Hg19::chr10:73848262..73848315,-p1@SPOCK2
Hg19::chr10:73848333..73848352,-p3@SPOCK2
Hg19::chr10:73848353..73848364,-p5@SPOCK2


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

No GOStat results

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 organism5.95e-49114
neural tube4.87e-4556
neural rod4.87e-4556
future spinal cord4.87e-4556
neural keel4.87e-4556
regional part of nervous system6.23e-4253
regional part of brain6.23e-4253
regional part of forebrain9.86e-3541
forebrain9.86e-3541
anterior neural tube9.86e-3541
future forebrain9.86e-3541
central nervous system6.42e-3381
brain6.01e-3168
future brain6.01e-3168
brain grey matter1.59e-2934
gray matter1.59e-2934
telencephalon2.31e-2934
cerebral hemisphere6.17e-2832
regional part of telencephalon1.94e-2732
nervous system2.09e-2789
neural plate4.15e-2782
presumptive neural plate4.15e-2782
neurectoderm7.11e-2586
cerebral cortex2.27e-2125
pallium2.27e-2125
regional part of cerebral cortex1.86e-2022
pre-chordal neural plate2.99e-2061
neocortex1.51e-1820
ecto-epithelium6.91e-18104
structure with developmental contribution from neural crest9.70e-14132
tube2.45e-12192
posterior neural tube3.24e-1115
chordal neural plate3.24e-1115
organ system subdivision1.43e-10223
neural nucleus1.38e-099
nucleus of brain1.38e-099
basal ganglion3.25e-099
nuclear complex of neuraxis3.25e-099
aggregate regional part of brain3.25e-099
collection of basal ganglia3.25e-099
cerebral subcortex3.25e-099
nephron tubule epithelium1.89e-0810
segmental subdivision of hindbrain2.14e-0812
hindbrain2.14e-0812
presumptive hindbrain2.14e-0812
gyrus8.89e-086
ectoderm-derived structure8.93e-08171
ectoderm8.93e-08171
presumptive ectoderm8.93e-08171
anatomical conduit1.34e-07240
telencephalic nucleus1.53e-077
brainstem1.60e-076
segmental subdivision of nervous system1.66e-0713
diencephalon9.97e-077
future diencephalon9.97e-077


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)
MA0003.10.371182
MA0004.10.32225
MA0006.11.05397
MA0007.10.305951
MA0009.10.756202
MA0014.10.0845458
MA0017.10.220105
MA0019.10.45566
MA0024.15.17813
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
MA0048.11.4241
MA0050.10.311321
MA0051.10.410316
MA0052.10.682867
MA0055.17.06395
MA0056.10
MA0057.10.3421
MA0058.10.240796
MA0059.10.673606
MA0060.10.103131
MA0061.10.28989
MA0063.10
MA0066.10.414559
MA0067.11.06751
MA0068.10.0633085
MA0069.10.741884
MA0070.10.731026
MA0071.12.63384
MA0072.10.726666
MA0073.10.00573911
MA0074.10.40963
MA0076.10.706813
MA0077.10.719193
MA0078.10.502027
MA0081.10.239862
MA0083.10.763502
MA0084.11.25286
MA0087.10.724294
MA0088.10.970753
MA0089.10
MA0090.10.266215
MA0091.10.324543
MA0092.10.291716
MA0093.10.558691
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
MA0111.11.39265
MA0113.10.467266
MA0114.10.418165
MA0115.10.992167
MA0116.10.140463
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
MA0139.10.961223
MA0140.10.376643
MA0141.10.238287
MA0142.10.570448
MA0143.10.467429
MA0144.10.124153
MA0145.11.05522
MA0146.10.79336
MA0147.12.01107
MA0148.10.344198
MA0149.10.367947
MA0062.20.0823902
MA0035.20.376007
MA0039.20.0035182
MA0138.20.503176
MA0002.20.316618
MA0137.20.20663
MA0104.21.66831
MA0047.20.440861
MA0112.20.416057
MA0065.20.733267
MA0150.10.261236
MA0151.10
MA0152.10.382565
MA0153.10.852412
MA0154.11.26237
MA0155.10.64751
MA0156.10.208455
MA0157.10.544523
MA0158.10
MA0159.12.01479
MA0160.10.940794
MA0161.10
MA0162.10.00310762
MA0163.10.0369192
MA0164.10.478818
MA0080.20.558855
MA0018.20.453345
MA0099.20.382887
MA0079.20.00539704
MA0102.21.28978
MA0258.10.117513
MA0259.10.891845
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
SUZ12#23512520.88157537960952.22261777511182e-067.96322393876169e-05



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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