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Coexpression cluster:C2505: Difference between revisions

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|tfbs_overrepresentation_jaspar=MA0003.1;0.720743,MA0004.1;0.71247,MA0006.1;0.532262,MA0007.1;0.6918,MA0009.1;1.20602,MA0014.1;0.0695829,MA0017.1;0.577281,MA0019.1;0.873355,MA0024.1;1.09684,MA0025.1;1.34373,MA0027.1;2.83281,MA0028.1;0.550763,MA0029.1;1.11704,MA0030.1;1.10506,MA0031.1;1.03735,MA0038.1;3.20044,MA0040.1;1.12314,MA0041.1;0.732902,MA0042.1;0.697662,MA0043.1;1.20635,MA0046.1;1.19471,MA0048.1;0.25531,MA0050.1;0.69864,MA0051.1;0.820063,MA0052.1;1.12718,MA0055.1;0.125954,MA0056.1;0,MA0057.1;0.248209,MA0058.1;0.605914,MA0059.1;0.604454,MA0060.1;1.80156,MA0061.1;0.360128,MA0063.1;0,MA0066.1;0.825101,MA0067.1;1.53181,MA0068.1;0.313194,MA0069.1;1.19071,MA0070.1;1.17908,MA0071.1;0.782546,MA0072.1;1.1744,MA0073.1;0.214613,MA0074.1;1.91637,MA0076.1;0.623864,MA0077.1;1.16637,MA0078.1;0.926725,MA0081.1;0.604638,MA0083.1;1.21381,MA0084.1;1.72172,MA0087.1;1.17185,MA0088.1;1.62583,MA0089.1;0,MA0090.1;0.640115,MA0091.1;0.715356,MA0092.1;0.673508,MA0093.1;0.535768,MA0095.1;0,MA0098.1;0,MA0100.1;0.83965,MA0101.1;0.539569,MA0103.1;0.521546,MA0105.1;0.232357,MA0106.1;0.869173,MA0107.1;0.453492,MA0108.2;1.03412,MA0109.1;0,MA0111.1;0.655276,MA0113.1;0.886811,MA0114.1;0.447443,MA0115.1;1.45393,MA0116.1;0.457606,MA0117.1;1.24497,MA0119.1;0.586221,MA0122.1;1.27173,MA0124.1;1.41151,MA0125.1;1.32534,MA0130.1;0,MA0131.1;0.94608,MA0132.1;0,MA0133.1;0,MA0135.1;1.23748,MA0136.1;0.832277,MA0139.1;0.344952,MA0140.1;0.779643,MA0141.1;0.602484,MA0142.1;1.00381,MA0143.1;0.887001,MA0144.1;1.09982,MA0145.1;9.01551,MA0146.1;0.221129,MA0147.1;0.46175,MA0148.1;0.739888,MA0149.1;3.0262,MA0062.2;0.353589,MA0035.2;0.778873,MA0039.2;0.10559,MA0138.2;2.1393,MA0002.2;0.379056,MA0137.2;1.37305,MA0104.2;0.392359,MA0047.2;0.856092,MA0112.2;0.551048,MA0065.2;0.199162,MA0150.1;2.59564,MA0151.1;0,MA0152.1;0.78681,MA0153.1;1.30799,MA0154.1;0.649108,MA0155.1;1.61785,MA0156.1;0.560797,MA0157.1;0.97481,MA0158.1;0,MA0159.1;0.462502,MA0160.1;0.756582,MA0161.1;0,MA0162.1;0.0928415,MA0163.1;0.0725493,MA0164.1;0.90014,MA0080.2;0.535868,MA0018.2;0.870662,MA0099.2;0.7872,MA0079.2;0.000248021,MA0102.2;1.75932,MA0258.1;0.418966,MA0259.1;0.471671,MA0442.1;0
}}
}}

Revision as of 20:42, 22 January 2013


Full id: C2505_Hepatocyte_lymph_vein_liver_Dendritic_left_submaxillary



Phase1 CAGE Peaks

Hg19::chr19:7796987..7797002,-p1@CLEC4G
Hg19::chr19:7797016..7797026,-p4@CLEC4G
Hg19::chr19:7797045..7797065,-p2@CLEC4G
Hg19::chr19:7828124..7828137,+p1@CLEC4M


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:0030369ICAM-3 receptor activity0.00151102607402967
GO:0005529sugar binding0.00151102607402967
GO:0046795intracellular virion transport0.00151102607402967
GO:0046794virion transport0.00151102607402967
GO:0046968peptide antigen transport0.00151102607402967
GO:0042607exogenous peptide antigen binding0.00151102607402967
GO:0019062virion attachment to host cell surface receptor0.00190159298712418
GO:0030246carbohydrate binding0.00190159298712418
GO:0046790virion binding0.00251826558870755
GO:0007159leukocyte adhesion0.00262406605701422
GO:0044409entry into host0.00262406605701422
GO:0030260entry into host cell0.00262406605701422
GO:0046718entry of virus into host cell0.00262406605701422
GO:0052126movement in host environment0.00262406605701422
GO:0019048virus-host interaction0.00262406605701422
GO:0051828entry into other organism during symbiotic interaction0.00262406605701422
GO:0019059initiation of viral infection0.00262406605701422
GO:0051806entry into cell of other organism during symbiotic interaction0.00262406605701422
GO:0052192movement in environment of other organism during symbiotic interaction0.00262406605701422
GO:0005537mannose binding0.00271944660842256
GO:0009405pathogenesis0.00280573694342962
GO:0009988cell-cell recognition0.0028841766369992
GO:0048029monosaccharide binding0.00334979634653054
GO:0042605peptide antigen binding0.00339900801690507
GO:0051701interaction with host0.00398793454926785
GO:0019079viral genome replication0.00505411638654445
GO:0044403symbiosis, encompassing mutualism through parasitism0.00517837325478262
GO:0044419interspecies interaction between organisms0.00517837325478262
GO:0008037cell recognition0.00588979241798844
GO:0015833peptide transport0.00588979241798844
GO:0019058viral infectious cycle0.007306251005552
GO:0022415viral reproductive process0.0080680090292174
GO:0048002antigen processing and presentation of peptide antigen0.0144015644791438
GO:0003823antigen binding0.023537887305015
GO:0010324membrane invagination0.0247348147228345
GO:0006897endocytosis0.0247348147228345
GO:0042277peptide binding0.0254059842469143
GO:0016044membrane organization and biogenesis0.0337381757692406
GO:0022414reproductive process0.0352928937058985
GO:0051704multi-organism process0.0375540220162645
GO:0016337cell-cell adhesion0.03817050394823
GO:0019882antigen processing and presentation0.0445188535659474



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
immature conventional dendritic cell5.73e-075
common dendritic progenitor5.73e-075
Uber Anatomy
Ontology termp-valuen
adult organism2.41e-34114
cardiac chamber6.75e-133
valve2.94e-123
cardiac mesenchyme2.94e-123
cardial valve2.94e-123
tunica intima2.94e-123
heart layer2.94e-123
endocardium2.94e-123
endocardial cushion2.94e-123
presumptive endocardium2.94e-123
cardiac atrium2.74e-092
future cardiac atrium2.74e-092
major salivary gland3.96e-092
atrioventricular valve8.16e-092
subdivision of digestive tract1.30e-08118
digestive system5.08e-07145
digestive tract5.08e-07145
primitive gut5.08e-07145
foregut6.10e-0787


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)
MA0003.10.720743
MA0004.10.71247
MA0006.10.532262
MA0007.10.6918
MA0009.11.20602
MA0014.10.0695829
MA0017.10.577281
MA0019.10.873355
MA0024.11.09684
MA0025.11.34373
MA0027.12.83281
MA0028.10.550763
MA0029.11.11704
MA0030.11.10506
MA0031.11.03735
MA0038.13.20044
MA0040.11.12314
MA0041.10.732902
MA0042.10.697662
MA0043.11.20635
MA0046.11.19471
MA0048.10.25531
MA0050.10.69864
MA0051.10.820063
MA0052.11.12718
MA0055.10.125954
MA0056.10
MA0057.10.248209
MA0058.10.605914
MA0059.10.604454
MA0060.11.80156
MA0061.10.360128
MA0063.10
MA0066.10.825101
MA0067.11.53181
MA0068.10.313194
MA0069.11.19071
MA0070.11.17908
MA0071.10.782546
MA0072.11.1744
MA0073.10.214613
MA0074.11.91637
MA0076.10.623864
MA0077.11.16637
MA0078.10.926725
MA0081.10.604638
MA0083.11.21381
MA0084.11.72172
MA0087.11.17185
MA0088.11.62583
MA0089.10
MA0090.10.640115
MA0091.10.715356
MA0092.10.673508
MA0093.10.535768
MA0095.10
MA0098.10
MA0100.10.83965
MA0101.10.539569
MA0103.10.521546
MA0105.10.232357
MA0106.10.869173
MA0107.10.453492
MA0108.21.03412
MA0109.10
MA0111.10.655276
MA0113.10.886811
MA0114.10.447443
MA0115.11.45393
MA0116.10.457606
MA0117.11.24497
MA0119.10.586221
MA0122.11.27173
MA0124.11.41151
MA0125.11.32534
MA0130.10
MA0131.10.94608
MA0132.10
MA0133.10
MA0135.11.23748
MA0136.10.832277
MA0139.10.344952
MA0140.10.779643
MA0141.10.602484
MA0142.11.00381
MA0143.10.887001
MA0144.11.09982
MA0145.19.01551
MA0146.10.221129
MA0147.10.46175
MA0148.10.739888
MA0149.13.0262
MA0062.20.353589
MA0035.20.778873
MA0039.20.10559
MA0138.22.1393
MA0002.20.379056
MA0137.21.37305
MA0104.20.392359
MA0047.20.856092
MA0112.20.551048
MA0065.20.199162
MA0150.12.59564
MA0151.10
MA0152.10.78681
MA0153.11.30799
MA0154.10.649108
MA0155.11.61785
MA0156.10.560797
MA0157.10.97481
MA0158.10
MA0159.10.462502
MA0160.10.756582
MA0161.10
MA0162.10.0928415
MA0163.10.0725493
MA0164.10.90014
MA0080.20.535868
MA0018.20.870662
MA0099.20.7872
MA0079.20.000248021
MA0102.21.75932
MA0258.10.418966
MA0259.10.471671
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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