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

Latest revision as of 11:14, 17 September 2013


Full id: C289_chorionic_skeletal_heart_Mast_amniotic_granulosa_left



Phase1 CAGE Peaks

Hg19::chr10:100150986..100150988,+p@chr10:100150986..100150988
+
Hg19::chr10:134275596..134275597,+p@chr10:134275596..134275597
+
Hg19::chr11:2150786..2150798,+p3@BC127839
Hg19::chr11:57154835..57154847,+p2@CU675194
Hg19::chr11:57154881..57154893,+p1@CU675194
Hg19::chr11:57154962..57154970,+p3@CU675194
Hg19::chr11:57156054..57156064,+p@chr11:57156054..57156064
+
Hg19::chr11:57156676..57156686,+p@chr11:57156676..57156686
+
Hg19::chr11:57156718..57156726,+p@chr11:57156718..57156726
+
Hg19::chr11:63488452..63488456,+p@chr11:63488452..63488456
+
Hg19::chr11:71710984..71711008,+p9@IL18BP
Hg19::chr11:71711013..71711028,+p6@IL18BP
Hg19::chr12:52301235..52301246,+p13@ACVRL1
Hg19::chr12:95267095..95267097,+p@chr12:95267095..95267097
+
Hg19::chr14:105359977..105359978,+p4@KIAA0284
Hg19::chr14:34516082..34516087,-p@chr14:34516082..34516087
-
Hg19::chr14:65105965..65105968,-p@chr14:65105965..65105968
-
Hg19::chr16:66959429..66959444,-p1@RRAD
Hg19::chr17:15686350..15686359,+p4@IL6STP1
Hg19::chr17:18164614..18164617,-p@chr17:18164614..18164617
-
Hg19::chr18:47766907..47766915,+p@chr18:47766907..47766915
+
Hg19::chr19:4210133..4210148,-p@chr19:4210133..4210148
-
Hg19::chr19:9783972..9783976,+p@chr19:9783972..9783976
+
Hg19::chr1:103299100..103299144,+p@chr1:103299100..103299144
+
Hg19::chr1:43988983..43989012,+p@chr1:43988983..43989012
+
Hg19::chr1:799209..799212,+p@chr1:799209..799212
+
Hg19::chr3:15493229..15493233,-p@chr3:15493229..15493233
-
Hg19::chr3:194215056..194215071,-p@chr3:194215056..194215071
-
Hg19::chr3:45596863..45596884,+p13@LIMD1
Hg19::chr3:4723000..4723006,+p@chr3:4723000..4723006
+
Hg19::chr3:97910197..97910206,+p@chr3:97910197..97910206
+
Hg19::chr5:115265770..115265773,-p@chr5:115265770..115265773
-
Hg19::chr5:127607810..127607838,-p@chr5:127607810..127607838
-
Hg19::chr5:176152899..176152904,+p@chr5:176152899..176152904
+
Hg19::chr5:2749492..2749495,-p@chr5:2749492..2749495
-
Hg19::chr6:161459302..161459304,+p@chr6:161459302..161459304
+
Hg19::chr6:36293751..36293753,-p@chr6:36293751..36293753
-
Hg19::chr6:4488206..4488213,+p@chr6:4488206..4488213
+
Hg19::chr6:80023101..80023112,-p3@uc003piw.1
Hg19::chr7:138848445..138848454,+p@chr7:138848445..138848454
+
Hg19::chr7:45932645..45932656,+p2@AF042356
Hg19::chr8:102466479..102466487,+p@chr8:102466479..102466487
+
Hg19::chr8:62490697..62490708,+p1@uc003xuk.2
Hg19::chr9:4299962..4299963,+p@chr9:4299962..4299963
+


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:0019838growth factor binding0.0135994348286824
GO:0019955cytokine binding0.0135994348286824
GO:0042007interleukin-18 binding0.0135994348286824
GO:0005057receptor signaling protein activity0.0174818995682708
GO:0035313wound healing, spreading of epidermal cells0.0174818995682708
GO:0050431transforming growth factor beta binding0.0174818995682708
GO:0051895negative regulation of focal adhesion formation0.0174818995682708
GO:0016361activin receptor activity, type I0.0176731998586883
GO:0051893regulation of focal adhesion formation0.0176731998586883
GO:0005025transforming growth factor beta receptor activity, type I0.0176731998586883
GO:0017002activin receptor activity0.0176731998586883
GO:0006349genetic imprinting0.0176731998586883
GO:0048185activin binding0.0176731998586883
GO:0007165signal transduction0.0176731998586883
GO:0001953negative regulation of cell-matrix adhesion0.0176731998586883
GO:0007167enzyme linked receptor protein signaling pathway0.0176731998586883
GO:0018445prothoracicotrophic hormone activity0.0176731998586883
GO:0007154cell communication0.0176731998586883
GO:0030547receptor inhibitor activity0.0176731998586883
GO:0048019receptor antagonist activity0.0176731998586883
GO:0005515protein binding0.0176731998586883
GO:0022408negative regulation of cell-cell adhesion0.018269524327721
GO:0005159insulin-like growth factor receptor binding0.018269524327721
GO:0030545receptor regulator activity0.018269524327721
GO:0042088T-helper 1 type immune response0.018269524327721
GO:0032502developmental process0.018269524327721
GO:0022407regulation of cell-cell adhesion0.018269524327721
GO:0048041focal adhesion formation0.018269524327721
GO:0001952regulation of cell-matrix adhesion0.018269524327721
GO:0046332SMAD binding0.021730292128721
GO:0004675transmembrane receptor protein serine/threonine kinase activity0.0229146203514971
GO:0005024transforming growth factor beta receptor activity0.0229146203514971
GO:0030336negative regulation of cell migration0.0234526246261097
GO:0051271negative regulation of cell motility0.0275452882691319
GO:0040013negative regulation of locomotion0.0279192182649181
GO:0007162negative regulation of cell adhesion0.0294004658922312
GO:0048856anatomical structure development0.0321170087531403
GO:0008286insulin receptor signaling pathway0.0342625499906871
GO:0005184neuropeptide hormone activity0.034424234422504
GO:0005520insulin-like growth factor binding0.0386319699557641
GO:0019965interleukin binding0.0396663923494634
GO:0007275multicellular organismal development0.041527046048951
GO:0008283cell proliferation0.0431655393324574
GO:0007179transforming growth factor beta receptor signaling pathway0.0461615641177144
GO:0008217regulation of blood pressure0.049627418817607



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
chorionic membrane mesenchymal stem cell9.61e-853
extraembryonic cell2.45e-2419
amnion mesenchymal stem cell5.08e-075
Uber Anatomy
Ontology termp-valuen
acellular anatomical structure9.61e-853
egg chorion9.61e-853
chorion1.32e-647
extraembryonic membrane1.37e-5014
membranous layer1.37e-5014
extraembryonic structure9.15e-3024
organ component layer4.31e-1166
placenta2.11e-084
allantois2.11e-084


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)
MA0003.10.0255241
MA0004.10.164226
MA0006.10.00959877
MA0007.10.340746
MA0009.10.295212
MA0014.10.0011936
MA0017.10.895568
MA0019.10.100079
MA0024.10.221542
MA0025.11.03013
MA0027.11.79461
MA0028.10.152894
MA0029.10.661529
MA0030.10.2268
MA0031.10.543895
MA0038.10.273665
MA0040.10.238542
MA0041.11.10794
MA0042.10.350053
MA0043.10.295444
MA0046.10.28722
MA0048.10.272755
MA0050.10.632267
MA0051.10.567488
MA0052.10.677023
MA0055.10.347204
MA0056.10
MA0057.10.364426
MA0058.10.217702
MA0059.10.215837
MA0060.10.461705
MA0061.10.523899
MA0063.10
MA0066.10.975125
MA0067.10.553259
MA0068.10.131442
MA0069.11.41712
MA0070.10.276295
MA0071.10.854197
MA0072.10.273057
MA0073.10.00059558
MA0074.10.958189
MA0076.10.097555
MA0077.10.737867
MA0078.10.124992
MA0081.10.216071
MA0083.11.47643
MA0084.10.721137
MA0087.10.271301
MA0088.10.131849
MA0089.10
MA0090.10.492569
MA0091.10.166703
MA0092.10.900695
MA0093.10.28089
MA0095.10
MA0098.10
MA0100.10.29024
MA0101.10.75277
MA0103.11.70836
MA0105.10.570651
MA0106.10.324061
MA0107.10.955971
MA0108.20.539294
MA0109.10
MA0111.10.119075
MA0113.10.345012
MA0114.10.445127
MA0115.10.487485
MA0116.11.64487
MA0117.10.32334
MA0119.10.19322
MA0122.10.343167
MA0124.10.452592
MA0125.10.384032
MA0130.10
MA0131.10.419238
MA0132.10
MA0133.10
MA0135.10.317863
MA0136.10.282045
MA0139.10.877306
MA0140.10.84614
MA0141.10.213332
MA0142.10.165691
MA0143.10.106183
MA0144.10.125436
MA0145.10.996757
MA0146.10.00572975
MA0147.10.164952
MA0148.10.188509
MA0149.12.28449
MA0062.20.0536664
MA0035.21.27718
MA0039.20.060178
MA0138.20.125638
MA0002.20.262615
MA0137.20.3219
MA0104.20.0854308
MA0047.20.0926231
MA0112.20.434463
MA0065.20.267356
MA0150.11.53403
MA0151.10
MA0152.10.233837
MA0153.10.370648
MA0154.10.406183
MA0155.10.668118
MA0156.10.163807
MA0157.10.149753
MA0158.10
MA0159.10.724369
MA0160.10.783048
MA0161.10
MA0162.10.0231338
MA0163.10.175999
MA0164.11.19995
MA0080.20.281066
MA0018.20.0988962
MA0099.21.81896
MA0079.20.000170238
MA0102.20.755388
MA0258.10.785272
MA0259.10.00470836
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

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