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{{Coexpression_clusters
{
|coexpression_dpi_cluster_scores_median=0,0

Latest revision as of 11:22, 17 September 2013


Full id: C412_serous_breast_papillotubular_ductus_seminal_kidney_clear



Phase1 CAGE Peaks

Hg19::chr11:13974012..13974015,-p@chr11:13974012..13974015
-
Hg19::chr11:61897513..61897534,+p4@INCENP
Hg19::chr11:61897578..61897585,+p10@INCENP
Hg19::chr16:34981388..34981402,+p1@ENST00000516373
Hg19::chr17:37809300..37809309,+p13@STARD3
Hg19::chr17:37856184..37856193,+p6@ERBB2
Hg19::chr17:37856299..37856329,+p1@ERBB2
Hg19::chr19:23732661..23732689,+p@chr19:23732661..23732689
+
Hg19::chr1:159836049..159836056,+p@chr1:159836049..159836056
+
Hg19::chr1:180240503..180240504,-p@chr1:180240503..180240504
-
Hg19::chr20:30943898..30943899,-p@chr20:30943898..30943899
-
Hg19::chr20:39536980..39536981,+p@chr20:39536980..39536981
+
Hg19::chr2:22353663..22353666,+p@chr2:22353663..22353666
+
Hg19::chr2:235157093..235157098,+p@chr2:235157093..235157098
+
Hg19::chr3:168726935..168726936,-p@chr3:168726935..168726936
-
Hg19::chr5:173377093..173377094,-p@chr5:173377093..173377094
-
Hg19::chr6:11768690..11768702,-p@chr6:11768690..11768702
-
Hg19::chr6:11768713..11768725,-p@chr6:11768713..11768725
-
Hg19::chr6:42724431..42724435,+p@chr6:42724431..42724435
+
Hg19::chr7:119683648..119683658,+p@chr7:119683648..119683658
+
Hg19::chr7:150006580..150006590,+p6@LRRC61
Hg19::chr7:150037547..150037552,-p10@RARRES2
Hg19::chr7:154497207..154497243,-p@chr7:154497207..154497243
-
Hg19::chr8:101588316..101588317,-p1@AK127517
Hg19::chr9:88496176..88496181,+p@chr9:88496176..88496181
+


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:0033087negative regulation of immature T cell proliferation0.00747674555516307
GO:0033080immature T cell proliferation in the thymus0.00747674555516307
GO:0033079immature T cell proliferation0.00747674555516307
GO:0033083regulation of immature T cell proliferation0.00747674555516307
GO:0033088negative regulation of immature T cell proliferation in the thymus0.00747674555516307
GO:0033084regulation of immature T cell proliferation in the thymus0.00747674555516307
GO:0005006epidermal growth factor receptor activity0.0168202015612282
GO:0005721centric heterochromatin0.0168202015612282
GO:0043125ErbB-3 class receptor binding0.0199335866525098
GO:0008045motor axon guidance0.0224236346827391
GO:0033077T cell differentiation in the thymus0.0313723029195121
GO:0007528neuromuscular junction development0.0313723029195121
GO:0016101diterpenoid metabolic process0.0313723029195121
GO:0017127cholesterol transporter activity0.0313723029195121
GO:0001523retinoid metabolic process0.0313723029195121
GO:0006700C21-steroid hormone biosynthetic process0.0313723029195121
GO:0004716receptor signaling protein tyrosine kinase activity0.0313723029195121
GO:0015248sterol transporter activity0.0313723029195121
GO:0030879mammary gland development0.0313723029195121
GO:0006721terpenoid metabolic process0.0313723029195121
GO:0008207C21-steroid hormone metabolic process0.0346241181710792
GO:0015485cholesterol binding0.0346241181710792
GO:0050679positive regulation of epithelial cell proliferation0.035064301385311
GO:0000792heterochromatin0.0373314928407595
GO:0008289lipid binding0.0413396373469942
GO:0007422peripheral nervous system development0.0413396373469942
GO:0042552myelination0.0417436404705552
GO:0032934sterol binding0.0417436404705552
GO:0031902late endosome membrane0.0417436404705552
GO:0050678regulation of epithelial cell proliferation0.0417436404705552
GO:0007272ensheathment of neurons0.0417436404705552
GO:0008366axon ensheathment0.0417436404705552
GO:0050673epithelial cell proliferation0.0417436404705552
GO:0042129regulation of T cell proliferation0.0417436404705552
GO:0000910cytokinesis0.0417436404705552
GO:0045765regulation of angiogenesis0.0417436404705552
GO:0042098T cell proliferation0.0417436404705552
GO:0050808synapse organization and biogenesis0.0417436404705552
GO:0001508regulation of action potential0.0417436404705552
GO:0044255cellular lipid metabolic process0.0417436404705552
GO:0030217T cell differentiation0.0417436404705552
GO:0048741skeletal muscle fiber development0.0417436404705552
GO:0050670regulation of lymphocyte proliferation0.0417436404705552
GO:0032944regulation of mononuclear cell proliferation0.0417436404705552
GO:0048747muscle fiber development0.0417436404705552
GO:0042446hormone biosynthetic process0.0418053836348106
GO:0006720isoprenoid metabolic process0.0428126721177308
GO:0048732gland development0.0428491605705884
GO:0006839mitochondrial transport0.043793229394858
GO:0005770late endosome0.0446891448334533
GO:0032943mononuclear cell proliferation0.0446891448334533
GO:0019748secondary metabolic process0.0446891448334533
GO:0046651lymphocyte proliferation0.0446891448334533
GO:0007411axon guidance0.0463340700446233
GO:0007059chromosome segregation0.0470624258525105
GO:0050863regulation of T cell activation0.0470624258525105
GO:0006629lipid metabolic process0.0480588986131011
GO:0030098lymphocyte differentiation0.0492722668622572
GO:0043406positive regulation of MAP kinase activity0.0497624591336918
GO:0007519skeletal muscle development0.0497624591336918
GO:0016324apical plasma membrane0.0497624591336918



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>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell of uterus2.83e-666
stromal cell of endometrium2.83e-666
stromal cell2.22e-1528
endo-epithelial cell1.07e-1042
endodermal cell4.33e-0858
Uber Anatomy
Ontology termp-valuen
uterus4.86e-2021
embryonic uterus3.41e-1922
internal female genitalia3.41e-1922
internal genitalia4.64e-1725
female reproductive organ5.76e-1237
female reproductive system5.76e-1237
female organism6.32e-1141
reproductive organ1.62e-0948
reproductive structure5.66e-0859
reproductive system5.66e-0859


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)
MA0003.10.0017346
MA0004.10.130779
MA0006.10.0525289
MA0007.10.120068
MA0009.10.480543
MA0014.10.0210893
MA0017.10.0687354
MA0019.10.227177
MA0024.10.391254
MA0025.10.599238
MA0027.12.03861
MA0028.10.0589063
MA0029.10.407394
MA0030.10.397801
MA0031.10.912186
MA0038.11.08158
MA0040.11.06051
MA0041.10.141769
MA0042.11.84685
MA0043.10.480818
MA0046.10.47108
MA0048.10.128228
MA0050.10.390696
MA0051.10.192868
MA0052.11.87776
MA0055.11.00704
MA0056.10
MA0057.10.118248
MA0058.10.0802423
MA0059.10.0796335
MA0060.11.32836
MA0061.10.15842
MA0063.10
MA0066.10.196017
MA0067.10.769322
MA0068.10.223662
MA0069.10.467738
MA0070.10.458064
MA0071.10.50749
MA0072.10.454189
MA0073.10.0561749
MA0074.10.561594
MA0076.10.0879186
MA0077.10.44756
MA0078.11.34069
MA0081.10.27336
MA0083.10.487092
MA0084.10.947429
MA0087.10.452083
MA0088.10.0453304
MA0089.10
MA0090.10.315775
MA0091.10.819573
MA0092.10.110943
MA0093.10.053707
MA0095.10
MA0098.10
MA0100.10.205224
MA0101.10.202181
MA0103.10.411939
MA0105.10.191442
MA0106.10.637762
MA0107.10.122976
MA0108.20.906703
MA0109.10
MA0111.10.102187
MA0113.10.236174
MA0114.10.118114
MA0115.10.697973
MA0116.10.872733
MA0117.10.513502
MA0119.10.537943
MA0122.10.53644
MA0124.10.659634
MA0125.11.42551
MA0130.10
MA0131.10.277285
MA0132.10
MA0133.10
MA0135.10.507125
MA0136.10.200538
MA0139.10.140093
MA0140.10.168354
MA0141.10.571374
MA0142.10.319458
MA0143.10.236302
MA0144.10.774342
MA0145.10.723202
MA0146.10.0288589
MA0147.10.031895
MA0148.10.876759
MA0149.10.162171
MA0062.20.0113502
MA0035.20.50217
MA0039.20.199497
MA0138.20.264522
MA0002.21.24813
MA0137.20.481909
MA0104.20.0784157
MA0047.20.617535
MA0112.20.477898
MA0065.21.26865
MA0150.10.307678
MA0151.10
MA0152.10.988857
MA0153.10.567879
MA0154.10.31593
MA0155.10.177814
MA0156.10.0625308
MA0157.10.807311
MA0158.10
MA0159.10.0320844
MA0160.10.916248
MA0161.10
MA0162.10.0253003
MA0163.10.00125667
MA0164.11.27209
MA0080.20.19841
MA0018.20.225392
MA0099.20.989801
MA0079.28.48191e-05
MA0102.20.983247
MA0258.11.07678
MA0259.10.0344451
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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