Coexpression cluster:C981: Difference between revisions
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{{Coexpression_clusters | 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metabolic process!0.00350288472860002!2625$GO:0042421!norepinephrine biosynthetic process!0.00350288472860002!2625$GO:0048485!sympathetic nervous system development!0.00467044422881899!2625$GO:0048483!autonomic nervous system development!0.00525417242194267!2625$GO:0042423!catecholamine biosynthetic process!0.0140096828629117!2625$GO:0042136!neurotransmitter biosynthetic process!0.0186779273270035!2625$GO:0043627!response to estrogen stimulus!0.0198400389723906!2625$GO:0006584!catecholamine metabolic process!0.0198400389723906!2625$GO:0018958!phenol metabolic process!0.0198400389723906!2625$GO:0001709!cell fate determination!0.0198400389723906!2625$GO:0042133!neurotransmitter metabolic process!0.0198400389723906!2625$GO:0042401!biogenic amine biosynthetic process!0.0198400389723906!2625$GO:0048545!response to steroid hormone stimulus!0.019928932469712!2625$GO:0042398!amino acid derivative biosynthetic process!0.0200707908551284!2625$GO:0042446!hormone biosynthetic 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metabolic process!0.0414706298862488!2625$GO:0006417!regulation of translation!0.0414706298862488!2625$GO:0031326!regulation of cellular biosynthetic process!0.0434401632898297!2625$GO:0009889!regulation of biosynthetic process!0.0457994655493675!2625$GO:0045893!positive regulation of transcription, 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12982,0.28215,0.279812,0.481032,0.491197,0.278645,0.439191,0.431751,0.586217,0.588503,0.535591,0.381036,0.491941,0.230489,0.653021,0.494548,0.462673,0.23568,0.213047,0.638022,0.394858,0.369527,0.569966,0.178571,0.568909,0.247225,0.48895,0.403105,0.366377,0.137919,0.540268,0.459344,0.697624|tfbs_overrepresentation_for_novel_motifs=0.920816,0.183537,0.341646,0.481684,0.301904,0.480078,1.36559,1.06773,0.555925,0.154405,0.450635,1.45571,0.152895,0.543352,0.300614,0.863056,0.774423,0.698835,0.491486,0.0766963,0.341703,0.180463,0.472508,1.46316,0.385586,0.619829,0.135503,0.470396,0.304828,0.122648,1.09762,0.810962,0.628961,0.469827,0.269459,0.570077,0.266487,0.481208,0.244807,0.174436,0.268162,0.413601,0.775279,0.809926,0.0775086,0.371118,0.555735,0.440085,0.186577,0.822946,0.63387,0.567337,0.0927889,0.887323,1.03948,0.546236,0.831988,0.514077,0.388089,0.513089,0.85167,0.558065,1.06063,0.746929,0.575742,0.712797,1.12756,1.49516,0.800646,1.33315,0.400869,0.573519,0.0911419,1.03748,0.149081,0.138565,2.54475,0.730167,0.797419,0.379656,0.50159,0.745864,0.575394,1.07768,0.986227,0.0958904,0.0757344,0.759942,0.659621,1.59442,1.22073,0.959334,0.827657,0.644398,0.302606,0.239285,1.51085,0.87,0.664183,0.106284,0.246049,0.822041,3.32465,0.778061,0.701386,0.446229,0.762347,0.539961,0.385342,0.286892,0.352381,0.861701,0.336372,0.459808,1.17281,0.732093,0.116216,0.428232,0.710479,0.650514,1.02923,0.657218,0.477387,0.586509,1.28328,0.730921,0.548418,0.83262,1.07171,1.94293,0.960022,0.432175,1.08604,1.42587,1.23359,0.364369,0.423593,0.470947,1.19123,2.04907,1.64679,1.15398,0.550118,0.866494,0.703126,0.505785,0.686615,1.88987,0.410382,0.224241,0.593875,0.0510299,0.960402,0.183004,0.557588,1.36372,0.643609,0.786331,1.00225,0.357927,1.15277,0.941964,0.796636,0.948033,0.71907,0.574616,0.213234,0.553354,0.146591|tfbs_overrepresentation_jaspar=MA0003.1;0.00718652,MA0004.1;0.455723,MA0006.1;0.300178,MA0007.1;0.437331,MA0009.1;0.918715,MA0014.1;0.00962431,MA0017.1;0.337901,MA0019.1;0.602411,MA0024.1;0.813542,MA0025.1;5.54305,MA0027.1;2.5321,MA0028.1;0.315574,MA0029.1;0.832916,MA0030.1;0.821423,MA0031.1;0.756713,MA0038.1;0.557409,MA0040.1;0.838784,MA0041.1;0.474018,MA0042.1;0.442535,MA0043.1;0.919032,MA0046.1;0.90778,MA0048.1;0.316923,MA0050.1;0.443405,MA0051.1;0.553205,MA0052.1;0.842664,MA0055.1;0.028436,MA0056.1;0,MA0057.1;0.0912556,MA0058.1;0.362328,MA0059.1;0.361075,MA0060.1;0.190336,MA0061.1;0.497495,MA0063.1;0,MA0066.1;0.557833,MA0067.1;1.23721,MA0068.1;1.93074,MA0069.1;0.903908,MA0070.1;0.892666,MA0071.1;0.518907,MA0072.1;0.888148,MA0073.1;0.0344109,MA0074.1;0.552456,MA0076.1;0.377799,MA0077.1;0.880402,MA0078.1;0.652193,MA0081.1;0.361233,MA0083.1;2.13567,MA0084.1;1.42483,MA0087.1;0.885691,MA0088.1;0.441522,MA0089.1;0,MA0090.1;0.391903,MA0091.1;0.458301,MA0092.1;0.421159,MA0093.1;0.303084,MA0095.1;0,MA0098.1;0,MA0100.1;0.571227,MA0101.1;0.30624,MA0103.1;0.291333,MA0105.1;0.0818021,MA0106.1;0.59853,MA0107.1;0.236528,MA0108.2;0.753643,MA0109.1;0,MA0111.1;1.04489,MA0113.1;1.49247,MA0114.1;0.231781,MA0115.1;1.1606,MA0116.1;0.239768,MA0117.1;0.956472,MA0119.1;0.345493,MA0122.1;0.982472,MA0124.1;1.11898,MA0125.1;1.0347,MA0130.1;0,MA0131.1;0.670358,MA0132.1;0,MA0133.1;0,MA0135.1;0.949204,MA0136.1;1.38624,MA0139.1;0.155155,MA0140.1;0.516266,MA0141.1;0.944441,MA0142.1;0.724856,MA0143.1;0.615094,MA0144.1;0.623945,MA0145.1;0.0613434,MA0146.1;0.0399277,MA0147.1;0.243042,MA0148.1;0.480298,MA0149.1;0.506665,MA0062.2;0.161302,MA0035.2;1.28264,MA0039.2;0.00915579,MA0138.2;0.653421,MA0002.2;0.179788,MA0137.2;0.321796,MA0104.2;0.189646,MA0047.2;0.586412,MA0112.2;0.0572179,MA0065.2;0.226158,MA0150.1;0.386144,MA0151.1;0,MA0152.1;0.52279,MA0153.1;1.01778,MA0154.1;0.274121,MA0155.1;0.0535085,MA0156.1;0.323987,MA0157.1;0.697424,MA0158.1;0,MA0159.1;0.243637,MA0160.1;0.495355,MA0161.1;0,MA0162.1;0.0163939,MA0163.1;0.0104024,MA0164.1;0.627336,MA0080.2;1.48508,MA0018.2;0.599912,MA0099.2;0.523145,MA0079.2;0.00126912,MA0102.2;1.46209,MA0258.1;0.209744,MA0259.1;0.25092,MA0442.1;0}} 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Latest revision as of 11:35, 17 September 2013
Full id: C981_choriocarcinoma_chorionic_pancreatic_placenta_amniotic_vagina_MCF7
Phase1 CAGE Peaks
| Hg19::chr10:71098164..71098182,+ | p@chr10:71098164..71098182 + |
| Hg19::chr10:8097468..8097478,+ | p16@GATA3 |
| Hg19::chr1:161059803..161059816,- | p7@PVRL4 |
| Hg19::chr1:161059882..161059905,- | p3@PVRL4 |
| Hg19::chr1:161059935..161059942,- | p@chr1:161059935..161059942 - |
| Hg19::chr2:228382337..228382369,+ | p@chr2:228382337..228382369 + |
| Hg19::chr5:80255192..80255201,+ | p@chr5:80255192..80255201 + |
| Hg19::chr9:112261641..112261646,+ | p@chr9:112261641..112261646 + |
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:0042415 | norepinephrine metabolic process | 0.00350288472860002 |
| GO:0042421 | norepinephrine biosynthetic process | 0.00350288472860002 |
| GO:0048485 | sympathetic nervous system development | 0.00467044422881899 |
| GO:0048483 | autonomic nervous system development | 0.00525417242194267 |
| GO:0042423 | catecholamine biosynthetic process | 0.0140096828629117 |
| GO:0042136 | neurotransmitter biosynthetic process | 0.0186779273270035 |
| GO:0043627 | response to estrogen stimulus | 0.0198400389723906 |
| GO:0006584 | catecholamine metabolic process | 0.0198400389723906 |
| GO:0018958 | phenol metabolic process | 0.0198400389723906 |
| GO:0001709 | cell fate determination | 0.0198400389723906 |
| GO:0042133 | neurotransmitter metabolic process | 0.0198400389723906 |
| GO:0042401 | biogenic amine biosynthetic process | 0.0198400389723906 |
| GO:0048545 | response to steroid hormone stimulus | 0.019928932469712 |
| GO:0042398 | amino acid derivative biosynthetic process | 0.0200707908551284 |
| GO:0042446 | hormone biosynthetic process | 0.0200707908551284 |
| GO:0042035 | regulation of cytokine biosynthetic process | 0.0248104870521948 |
| GO:0042089 | cytokine biosynthetic process | 0.0248104870521948 |
| GO:0042107 | cytokine metabolic process | 0.0248104870521948 |
| GO:0045165 | cell fate commitment | 0.0248104870521948 |
| GO:0006576 | biogenic amine metabolic process | 0.0248104870521948 |
| GO:0009725 | response to hormone stimulus | 0.0248104870521948 |
| GO:0001505 | regulation of neurotransmitter levels | 0.0248104870521948 |
| GO:0042445 | hormone metabolic process | 0.0262372211764849 |
| GO:0006575 | amino acid derivative metabolic process | 0.0262372211764849 |
| GO:0001816 | cytokine production | 0.0316138775295708 |
| GO:0009309 | amine biosynthetic process | 0.0320091784237637 |
| GO:0050954 | sensory perception of mechanical stimulus | 0.032963518626922 |
| GO:0007605 | sensory perception of sound | 0.032963518626922 |
| GO:0044271 | nitrogen compound biosynthetic process | 0.0354356923500112 |
| GO:0006725 | aromatic compound metabolic process | 0.0414706298862488 |
| GO:0006417 | regulation of translation | 0.0414706298862488 |
| GO:0031326 | regulation of cellular biosynthetic process | 0.0434401632898297 |
| GO:0009889 | regulation of biosynthetic process | 0.0457994655493675 |
| GO:0045893 | positive regulation of transcription, DNA-dependent | 0.0457994655493675 |
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 |
|---|---|---|
| chorionic membrane mesenchymal stem cell | 1.41e-46 | 3 |
| germ line cell | 2.32e-20 | 7 |
| germ cell | 2.32e-20 | 7 |
| extraembryonic cell | 3.48e-20 | 19 |
| amnion mesenchymal stem cell | 3.65e-13 | 5 |
| Ontology term | p-value | n |
|---|---|---|
| acellular anatomical structure | 1.41e-46 | 3 |
| egg chorion | 1.41e-46 | 3 |
| extraembryonic membrane | 4.67e-39 | 14 |
| membranous layer | 4.67e-39 | 14 |
| chorion | 2.15e-35 | 7 |
| extraembryonic structure | 9.22e-23 | 24 |
| amnion | 1.13e-09 | 7 |
| somatic layer of lateral plate mesoderm | 1.42e-08 | 8 |
| organ component layer | 3.86e-08 | 66 |
| Ontology term | p-value | n |
|---|---|---|
| islet cell tumor | 1.04e-16 | 1 |
| endocrine pancreas cancer | 1.04e-16 | 1 |
| pancreatic endocrine carcinoma | 1.04e-16 | 1 |
| germ cell and embryonal cancer | 7.03e-07 | 22 |
| germ cell cancer | 7.03e-07 | 22 |
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 | 0.00718652 |
| MA0004.1 | 0.455723 |
| MA0006.1 | 0.300178 |
| MA0007.1 | 0.437331 |
| MA0009.1 | 0.918715 |
| MA0014.1 | 0.00962431 |
| MA0017.1 | 0.337901 |
| MA0019.1 | 0.602411 |
| MA0024.1 | 0.813542 |
| MA0025.1 | 5.54305 |
| MA0027.1 | 2.5321 |
| MA0028.1 | 0.315574 |
| MA0029.1 | 0.832916 |
| MA0030.1 | 0.821423 |
| MA0031.1 | 0.756713 |
| MA0038.1 | 0.557409 |
| MA0040.1 | 0.838784 |
| MA0041.1 | 0.474018 |
| MA0042.1 | 0.442535 |
| MA0043.1 | 0.919032 |
| MA0046.1 | 0.90778 |
| MA0048.1 | 0.316923 |
| MA0050.1 | 0.443405 |
| MA0051.1 | 0.553205 |
| MA0052.1 | 0.842664 |
| MA0055.1 | 0.028436 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0912556 |
| MA0058.1 | 0.362328 |
| MA0059.1 | 0.361075 |
| MA0060.1 | 0.190336 |
| MA0061.1 | 0.497495 |
| MA0063.1 | 0 |
| MA0066.1 | 0.557833 |
| MA0067.1 | 1.23721 |
| MA0068.1 | 1.93074 |
| MA0069.1 | 0.903908 |
| MA0070.1 | 0.892666 |
| MA0071.1 | 0.518907 |
| MA0072.1 | 0.888148 |
| MA0073.1 | 0.0344109 |
| MA0074.1 | 0.552456 |
| MA0076.1 | 0.377799 |
| MA0077.1 | 0.880402 |
| MA0078.1 | 0.652193 |
| MA0081.1 | 0.361233 |
| MA0083.1 | 2.13567 |
| MA0084.1 | 1.42483 |
| MA0087.1 | 0.885691 |
| MA0088.1 | 0.441522 |
| MA0089.1 | 0 |
| MA0090.1 | 0.391903 |
| MA0091.1 | 0.458301 |
| MA0092.1 | 0.421159 |
| MA0093.1 | 0.303084 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.571227 |
| MA0101.1 | 0.30624 |
| MA0103.1 | 0.291333 |
| MA0105.1 | 0.0818021 |
| MA0106.1 | 0.59853 |
| MA0107.1 | 0.236528 |
| MA0108.2 | 0.753643 |
| MA0109.1 | 0 |
| MA0111.1 | 1.04489 |
| MA0113.1 | 1.49247 |
| MA0114.1 | 0.231781 |
| MA0115.1 | 1.1606 |
| MA0116.1 | 0.239768 |
| MA0117.1 | 0.956472 |
| MA0119.1 | 0.345493 |
| MA0122.1 | 0.982472 |
| MA0124.1 | 1.11898 |
| MA0125.1 | 1.0347 |
| MA0130.1 | 0 |
| MA0131.1 | 0.670358 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.949204 |
| MA0136.1 | 1.38624 |
| MA0139.1 | 0.155155 |
| MA0140.1 | 0.516266 |
| MA0141.1 | 0.944441 |
| MA0142.1 | 0.724856 |
| MA0143.1 | 0.615094 |
| MA0144.1 | 0.623945 |
| MA0145.1 | 0.0613434 |
| MA0146.1 | 0.0399277 |
| MA0147.1 | 0.243042 |
| MA0148.1 | 0.480298 |
| MA0149.1 | 0.506665 |
| MA0062.2 | 0.161302 |
| MA0035.2 | 1.28264 |
| MA0039.2 | 0.00915579 |
| MA0138.2 | 0.653421 |
| MA0002.2 | 0.179788 |
| MA0137.2 | 0.321796 |
| MA0104.2 | 0.189646 |
| MA0047.2 | 0.586412 |
| MA0112.2 | 0.0572179 |
| MA0065.2 | 0.226158 |
| MA0150.1 | 0.386144 |
| MA0151.1 | 0 |
| MA0152.1 | 0.52279 |
| MA0153.1 | 1.01778 |
| MA0154.1 | 0.274121 |
| MA0155.1 | 0.0535085 |
| MA0156.1 | 0.323987 |
| MA0157.1 | 0.697424 |
| MA0158.1 | 0 |
| MA0159.1 | 0.243637 |
| MA0160.1 | 0.495355 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0163939 |
| MA0163.1 | 0.0104024 |
| MA0164.1 | 0.627336 |
| MA0080.2 | 1.48508 |
| MA0018.2 | 0.599912 |
| MA0099.2 | 0.523145 |
| MA0079.2 | 0.00126912 |
| MA0102.2 | 1.46209 |
| MA0258.1 | 0.209744 |
| MA0259.1 | 0.25092 |
| 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.
