Coexpression cluster:C3833: Difference between revisions
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{{Coexpression_clusters | 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virion transport!0.0010891322265395!30835$GO:0046794!virion transport!0.0010891322265395!30835$GO:0046968!peptide antigen transport!0.0010891322265395!30835$GO:0042607!exogenous peptide antigen binding!0.0010891322265395!30835$GO:0019062!virion attachment to host cell surface receptor!0.0013069586718474!30835$GO:0046790!virion binding!0.00140946523434524!30835$GO:0007159!leukocyte adhesion!0.00140946523434524!30835$GO:0044409!entry into host!0.00140946523434524!30835$GO:0030260!entry into host cell!0.00140946523434524!30835$GO:0046718!entry of virus into host cell!0.00140946523434524!30835$GO:0007157!heterophilic cell adhesion!0.00140946523434524!30835$GO:0052126!movement in host environment!0.00140946523434524!30835$GO:0019048!virus-host interaction!0.00140946523434524!30835$GO:0051828!entry into other organism during symbiotic interaction!0.00140946523434524!30835$GO:0019059!initiation of viral infection!0.00140946523434524!30835$GO:0051806!entry into cell of other organism during symbiotic interaction!0.00140946523434524!30835$GO:0052192!movement in environment of other organism during symbiotic interaction!0.00140946523434524!30835$GO:0005537!mannose binding!0.00145217630205267!30835$GO:0009405!pathogenesis!0.00149039146789616!30835$GO:0009988!cell-cell recognition!0.0015247851171553!30835$GO:0048029!monosaccharide binding!0.00176335693820681!30835$GO:0042605!peptide antigen binding!0.001782216370701!30835$GO:0051701!interaction with host!0.00208355730294514!30835$GO:0019079!viral genome replication!0.00263206954747047!30835$GO:0044403!symbiosis, encompassing mutualism through parasitism!0.00268094086532801!30835$GO:0044419!interspecies interaction between organisms!0.00268094086532801!30835$GO:0008037!cell recognition!0.0030340112025029!30835$GO:0015833!peptide transport!0.0030340112025029!30835$GO:0019058!viral infectious cycle!0.0037556283673776!30835$GO:0022415!viral reproductive process!0.00413870246085011!30835$GO:0048002!antigen processing and presentation of peptide antigen!0.00737799250236437!30835$GO:0003823!antigen binding!0.0120485252560932!30835$GO:0010324!membrane invagination!0.012621120507546!30835$GO:0006897!endocytosis!0.012621120507546!30835$GO:0042277!peptide binding!0.0129451144640124!30835$GO:0016044!membrane organization and biogenesis!0.0171840862409566!30835$GO:0022414!reproductive process!0.0179559637348405!30835$GO:0051704!multi-organism process!0.0188964441304604!30835$GO:0016337!cell-cell adhesion!0.0188964441304604!30835$GO:0005529!sugar binding!0.0188964441304604!30835$GO:0019882!antigen processing and presentation!0.0220482865372631!30835$GO:0030246!carbohydrate binding!0.0247907240136135!30835$GO:0016192!vesicle-mediated transport!0.0306983315945553!30835$GO:0046907!intracellular transport!0.0450504693704976!30835$GO:0022610!biological adhesion!0.0454594320642575!30835$GO:0007155!cell 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60658,0.206239,0.19924,0.28689,0.236464,0.325148,0.115817,0.218052,0.223831,0.11528,0.194982,0.190993,0.281727,0.283218,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.316866,0.171683,0.158847,0.271275,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.205954,0.361435|tfbs_overrepresentation_for_novel_motifs=0.699513,0.442617,0.690871,0.855819,0.641468,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,0.639839,0.667627,1.17594,0.575162,0.452865,0.305559,0.69094,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,0.388328,0.795576,1.21459,0.534793,0.439574,0.599922,0.427404,0.596053,0.855276,0.567465,0.469078,0.598234,0.777097,0.718382,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.893117,1.29475,1.45259,0.928548,0.650353,0.892517,1.0078,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,1.25415,0.333216,1.45054,0.430728,0.414196,1.81344,1.12884,1.20029,0.73687,0.459024,1.14559,0.960908,1.24629,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,0.543775,0.642354,0.560075,0.450952,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,0.703975,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,1.35006,1.44203,1.0504,0.850918,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,1.82176,0.539692,0.318511,0.250511,1.37083,0.481626,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,0.714443,1.11698,0.960047,0.524529,0.936473,0.0768232|tfbs_overrepresentation_jaspar=MA0003.1;0.178364,MA0004.1;0.826076,MA0006.1;0.639288,MA0007.1;0.804807,MA0009.1;1.3275,MA0014.1;0.118426,MA0017.1;0.686276,MA0019.1;0.990656,MA0024.1;1.21731,MA0025.1;1.46617,MA0027.1;2.95767,MA0028.1;0.658629,MA0029.1;1.23771,MA0030.1;1.22561,MA0031.1;1.15713,MA0038.1;0.94098,MA0040.1;1.24388,MA0041.1;0.847069,MA0042.1;0.810843,MA0043.1;1.32783,MA0046.1;1.31611,MA0048.1;0.341392,MA0050.1;0.81185,MA0051.1;0.936307,MA0052.1;1.24796,MA0055.1;0.557638,MA0056.1;0,MA0057.1;0.333427,MA0058.1;0.716037,MA0059.1;0.714521,MA0060.1;0.492218,MA0061.1;0.456531,MA0063.1;0,MA0066.1;0.941452,MA0067.1;1.65513,MA0068.1;0.405474,MA0069.1;1.31207,MA0070.1;1.30033,MA0071.1;0.897953,MA0072.1;1.29561,MA0073.1;0.211629,MA0074.1;0.935474,MA0076.1;1.74184,MA0077.1;1.28751,MA0078.1;1.04495,MA0081.1;0.714712,MA0083.1;1.33535,MA0084.1;1.84562,MA0087.1;1.29304,MA0088.1;1.31954,MA0089.1;0,MA0090.1;0.751469,MA0091.1;1.93651,MA0092.1;0.785956,MA0093.1;0.642957,MA0095.1;0,MA0098.1;0,MA0100.1;0.956299,MA0101.1;0.646932,MA0103.1;0.628063,MA0105.1;0.31555,MA0106.1;0.986396,MA0107.1;0.556367,MA0108.2;1.15387,MA0109.1;0,MA0111.1;0.767139,MA0113.1;1.00436,MA0114.1;0.549955,MA0115.1;1.57693,MA0116.1;0.560723,MA0117.1;1.36676,MA0119.1;0.695578,MA0122.1;1.39371,MA0124.1;1.53432,MA0125.1;1.44766,MA0130.1;0,MA0131.1;1.06461,MA0132.1;0,MA0133.1;0,MA0135.1;1.35921,MA0136.1;0.948776,MA0139.1;0.440097,MA0140.1;0.894983,MA0141.1;0.712476,MA0142.1;1.12317,MA0143.1;1.00455,MA0144.1;0.531867,MA0145.1;0.273764,MA0146.1;0.107247,MA0147.1;0.565108,MA0148.1;0.854239,MA0149.1;0.884158,MA0062.2;1.141,MA0035.2;0.894194,MA0039.2;0.0526989,MA0138.2;1.04628,MA0002.2;0.476938,MA0137.2;1.60005,MA0104.2;0.491226,MA0047.2;0.973066,MA0112.2;0.264678,MA0065.2;0.277623,MA0150.1;0.744617,MA0151.1;0,MA0152.1;0.902317,MA0153.1;1.43021,MA0154.1;0.838867,MA0155.1;0.711948,MA0156.1;0.669101,MA0157.1;1.09377,MA0158.1;0,MA0159.1;0.565904,MA0160.1;0.871361,MA0161.1;0,MA0162.1;0.149099,MA0163.1;0.122425,MA0164.1;1.01792,MA0080.2;1.55139,MA0018.2;0.987913,MA0099.2;0.902716,MA0079.2;0.00160703,MA0102.2;1.88331,MA0258.1;0.519674,MA0259.1;0.575594,MA0442.1;0}} 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Latest revision as of 12:33, 17 September 2013
Full id: C3833_Dendritic_lymph_dura_CD14_duodenum_vein_left
Phase1 CAGE Peaks
| Hg19::chr19:7805780..7805799,- | p@chr19:7805780..7805799 - |
| Hg19::chr19:7807611..7807619,- | p1@AK057212 |
| Hg19::chr19:7812412..7812426,- | p2@CD209 |
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 ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0046795 | intracellular virion transport | 0.0010891322265395 |
| GO:0046794 | virion transport | 0.0010891322265395 |
| GO:0046968 | peptide antigen transport | 0.0010891322265395 |
| GO:0042607 | exogenous peptide antigen binding | 0.0010891322265395 |
| GO:0019062 | virion attachment to host cell surface receptor | 0.0013069586718474 |
| GO:0046790 | virion binding | 0.00140946523434524 |
| GO:0007159 | leukocyte adhesion | 0.00140946523434524 |
| GO:0044409 | entry into host | 0.00140946523434524 |
| GO:0030260 | entry into host cell | 0.00140946523434524 |
| GO:0046718 | entry of virus into host cell | 0.00140946523434524 |
| GO:0007157 | heterophilic cell adhesion | 0.00140946523434524 |
| GO:0052126 | movement in host environment | 0.00140946523434524 |
| GO:0019048 | virus-host interaction | 0.00140946523434524 |
| GO:0051828 | entry into other organism during symbiotic interaction | 0.00140946523434524 |
| GO:0019059 | initiation of viral infection | 0.00140946523434524 |
| GO:0051806 | entry into cell of other organism during symbiotic interaction | 0.00140946523434524 |
| GO:0052192 | movement in environment of other organism during symbiotic interaction | 0.00140946523434524 |
| GO:0005537 | mannose binding | 0.00145217630205267 |
| GO:0009405 | pathogenesis | 0.00149039146789616 |
| GO:0009988 | cell-cell recognition | 0.0015247851171553 |
| GO:0048029 | monosaccharide binding | 0.00176335693820681 |
| GO:0042605 | peptide antigen binding | 0.001782216370701 |
| GO:0051701 | interaction with host | 0.00208355730294514 |
| GO:0019079 | viral genome replication | 0.00263206954747047 |
| GO:0044403 | symbiosis, encompassing mutualism through parasitism | 0.00268094086532801 |
| GO:0044419 | interspecies interaction between organisms | 0.00268094086532801 |
| GO:0008037 | cell recognition | 0.0030340112025029 |
| GO:0015833 | peptide transport | 0.0030340112025029 |
| GO:0019058 | viral infectious cycle | 0.0037556283673776 |
| GO:0022415 | viral reproductive process | 0.00413870246085011 |
| GO:0048002 | antigen processing and presentation of peptide antigen | 0.00737799250236437 |
| GO:0003823 | antigen binding | 0.0120485252560932 |
| GO:0010324 | membrane invagination | 0.012621120507546 |
| GO:0006897 | endocytosis | 0.012621120507546 |
| GO:0042277 | peptide binding | 0.0129451144640124 |
| GO:0016044 | membrane organization and biogenesis | 0.0171840862409566 |
| GO:0022414 | reproductive process | 0.0179559637348405 |
| GO:0051704 | multi-organism process | 0.0188964441304604 |
| GO:0016337 | cell-cell adhesion | 0.0188964441304604 |
| GO:0005529 | sugar binding | 0.0188964441304604 |
| GO:0019882 | antigen processing and presentation | 0.0220482865372631 |
| GO:0030246 | carbohydrate binding | 0.0247907240136135 |
| GO:0016192 | vesicle-mediated transport | 0.0306983315945553 |
| GO:0046907 | intracellular transport | 0.0450504693704976 |
| GO:0022610 | biological adhesion | 0.0454594320642575 |
| GO:0007155 | cell adhesion | 0.0454594320642575 |
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>
| Ontology term | p-value | n |
|---|---|---|
| macrophage | 1.16e-19 | 6 |
| monopoietic cell | 1.70e-07 | 59 |
| monocyte | 1.70e-07 | 59 |
| monoblast | 1.70e-07 | 59 |
| promonocyte | 1.70e-07 | 59 |
| macrophage dendritic cell progenitor | 3.73e-07 | 61 |
| Ontology term | p-value | n |
|---|---|---|
| adult organism | 9.32e-21 | 114 |
| cardiac chamber | 1.35e-10 | 3 |
| cardiac atrium | 1.24e-07 | 2 |
| future cardiac atrium | 1.24e-07 | 2 |
| immune system | 1.49e-07 | 93 |
| Ontology term | p-value | n |
|---|---|---|
| heart disease | 4.02e-07 | 2 |
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) |
|---|---|
| MA0003.1 | 0.178364 |
| MA0004.1 | 0.826076 |
| MA0006.1 | 0.639288 |
| MA0007.1 | 0.804807 |
| MA0009.1 | 1.3275 |
| MA0014.1 | 0.118426 |
| MA0017.1 | 0.686276 |
| MA0019.1 | 0.990656 |
| MA0024.1 | 1.21731 |
| MA0025.1 | 1.46617 |
| MA0027.1 | 2.95767 |
| MA0028.1 | 0.658629 |
| MA0029.1 | 1.23771 |
| MA0030.1 | 1.22561 |
| MA0031.1 | 1.15713 |
| MA0038.1 | 0.94098 |
| MA0040.1 | 1.24388 |
| MA0041.1 | 0.847069 |
| MA0042.1 | 0.810843 |
| MA0043.1 | 1.32783 |
| MA0046.1 | 1.31611 |
| MA0048.1 | 0.341392 |
| MA0050.1 | 0.81185 |
| MA0051.1 | 0.936307 |
| MA0052.1 | 1.24796 |
| MA0055.1 | 0.557638 |
| MA0056.1 | 0 |
| MA0057.1 | 0.333427 |
| MA0058.1 | 0.716037 |
| MA0059.1 | 0.714521 |
| MA0060.1 | 0.492218 |
| MA0061.1 | 0.456531 |
| MA0063.1 | 0 |
| MA0066.1 | 0.941452 |
| MA0067.1 | 1.65513 |
| MA0068.1 | 0.405474 |
| MA0069.1 | 1.31207 |
| MA0070.1 | 1.30033 |
| MA0071.1 | 0.897953 |
| MA0072.1 | 1.29561 |
| MA0073.1 | 0.211629 |
| MA0074.1 | 0.935474 |
| MA0076.1 | 1.74184 |
| MA0077.1 | 1.28751 |
| MA0078.1 | 1.04495 |
| MA0081.1 | 0.714712 |
| MA0083.1 | 1.33535 |
| MA0084.1 | 1.84562 |
| MA0087.1 | 1.29304 |
| MA0088.1 | 1.31954 |
| MA0089.1 | 0 |
| MA0090.1 | 0.751469 |
| MA0091.1 | 1.93651 |
| MA0092.1 | 0.785956 |
| MA0093.1 | 0.642957 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.956299 |
| MA0101.1 | 0.646932 |
| MA0103.1 | 0.628063 |
| MA0105.1 | 0.31555 |
| MA0106.1 | 0.986396 |
| MA0107.1 | 0.556367 |
| MA0108.2 | 1.15387 |
| MA0109.1 | 0 |
| MA0111.1 | 0.767139 |
| MA0113.1 | 1.00436 |
| MA0114.1 | 0.549955 |
| MA0115.1 | 1.57693 |
| MA0116.1 | 0.560723 |
| MA0117.1 | 1.36676 |
| MA0119.1 | 0.695578 |
| MA0122.1 | 1.39371 |
| MA0124.1 | 1.53432 |
| MA0125.1 | 1.44766 |
| MA0130.1 | 0 |
| MA0131.1 | 1.06461 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.35921 |
| MA0136.1 | 0.948776 |
| MA0139.1 | 0.440097 |
| MA0140.1 | 0.894983 |
| MA0141.1 | 0.712476 |
| MA0142.1 | 1.12317 |
| MA0143.1 | 1.00455 |
| MA0144.1 | 0.531867 |
| MA0145.1 | 0.273764 |
| MA0146.1 | 0.107247 |
| MA0147.1 | 0.565108 |
| MA0148.1 | 0.854239 |
| MA0149.1 | 0.884158 |
| MA0062.2 | 1.141 |
| MA0035.2 | 0.894194 |
| MA0039.2 | 0.0526989 |
| MA0138.2 | 1.04628 |
| MA0002.2 | 0.476938 |
| MA0137.2 | 1.60005 |
| MA0104.2 | 0.491226 |
| MA0047.2 | 0.973066 |
| MA0112.2 | 0.264678 |
| MA0065.2 | 0.277623 |
| MA0150.1 | 0.744617 |
| MA0151.1 | 0 |
| MA0152.1 | 0.902317 |
| MA0153.1 | 1.43021 |
| MA0154.1 | 0.838867 |
| MA0155.1 | 0.711948 |
| MA0156.1 | 0.669101 |
| MA0157.1 | 1.09377 |
| MA0158.1 | 0 |
| MA0159.1 | 0.565904 |
| MA0160.1 | 0.871361 |
| MA0161.1 | 0 |
| MA0162.1 | 0.149099 |
| MA0163.1 | 0.122425 |
| MA0164.1 | 1.01792 |
| MA0080.2 | 1.55139 |
| MA0018.2 | 0.987913 |
| MA0099.2 | 0.902716 |
| MA0079.2 | 0.00160703 |
| MA0102.2 | 1.88331 |
| MA0258.1 | 0.519674 |
| MA0259.1 | 0.575594 |
| MA0442.1 | 0 |
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.
