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Coexpression cluster:C614: Difference between revisions

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{{Coexpression_clusters
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00496701,0.618619|tfbs_overrepresentation_for_novel_motifs=0.554539,0.1536,0.183956,0.297884,0.911588,0.803906,0.360887,0.0785261,0.0771434,0.0971722,0.271739,0.398649,0.0551804,0.350994,0.465119,0.169541,0.560096,0.117033,0.220719,0.0824773,1.63625,0.681782,0.789382,0.150321,0.218509,0.418678,0.695716,0.288329,0.156049,0.0390294,0.254115,0.594213,0.096776,0.452879,0.130292,0.247035,0.12818,0.29748,0.113038,0.881025,0.806754,0.241157,0.289954,0.151865,0.00979465,0.206995,0.361827,0.262957,0.26404,0.15614,0.431291,0.372023,0.0249724,0.666176,0.811691,0.353512,0.480541,0.325599,0.987553,0.324748,0.632472,0.363871,0.26694,0.534578,0.379438,0.503101,0.896916,1.25738,0.584559,1.09778,0.230809,0.278952,0.0242598,0.80977,0.0530506,0.178887,0.658179,0.519091,0.581542,1.15217,0.849149,0.533593,0.37913,0.0800936,0.760489,0.00225746,0.0810924,0.0370991,0.454557,1.35556,0.98765,0.734737,0.609873,0.679242,0.154399,0.109261,0.0605346,0.649779,0.458696,0.12702,0.113893,0.6046,0.644537,0.563483,1.23371,0.268065,0.548871,0.348037,1.16972,0.142849,1.06793,0.641937,0.179896,0.765049,0.940917,0.12714,0.0638634,0.253155,0.500972,0.336456,0.801818,0.452379,0.294241,0.388967,1.04884,0.519787,0.355419,0.614537,0.842806,0.109858,0.735394,0.712269,0.856671,0.386057,1.00021,0.138272,1.99112,0.288795,0.95886,1.80749,1.40745,0.922589,0.938959,0.646464,0.494226,0.318465,0.47912,1.64894,0.238532,0.326467,0.020982,0.00934991,0.735758,0.541074,0.363452,1.12781,0.440071,0.443316,1.17064,0.196611,0.921409,0.718143,0.580811,0.199028,0.508869,0.378443,0.306931,0.35974,0.212432|tfbs_overrepresentation_jaspar=MA0003.1;0.00286173,MA0004.1;0.275994,MA0006.1;0.152601,MA0007.1;0.7221,MA0009.1;0.695988,MA0014.1;0.00418733,MA0017.1;1.02314,MA0019.1;0.403106,MA0024.1;0.59663,MA0025.1;0.824398,MA0027.1;2.28954,MA0028.1;0.164086,MA0029.1;0.614815,MA0030.1;0.604021,MA0031.1;0.543644,MA0038.1;0.363295,MA0040.1;0.620334,MA0041.1;0.291389,MA0042.1;0.264992,MA0043.1;0.69629,MA0046.1;0.685589,MA0048.1;0.0262025,MA0050.1;0.265714,MA0051.1;0.944936,MA0052.1;0.623986,MA0055.1;0.0207496,MA0056.1;0,MA0057.1;0.10396,MA0058.1;0.200063,MA0059.1;0.57771,MA0060.1;0.0773489,MA0061.1;0.224865,MA0063.1;0,MA0066.1;0.363668,MA0067.1;1.00375,MA0068.1;0.169955,MA0069.1;1.6324,MA0070.1;0.671241,MA0071.1;0.329767,MA0072.1;0.666958,MA0073.1;0.000431279,MA0074.1;0.358953,MA0076.1;0.212295,MA0077.1;0.65962,MA0078.1;0.447828,MA0081.1;1.72153,MA0083.1;0.703169,MA0084.1;1.18798,MA0087.1;0.664629,MA0088.1;0.14098,MA0089.1;0,MA0090.1;0.223576,MA0091.1;0.762163,MA0092.1;0.691297,MA0093.1;0.469677,MA0095.1;0,MA0098.1;0,MA0100.1;0.375452,MA0101.1;0.1571,MA0103.1;0.146091,MA0105.1;0.0203556,MA0106.1;0.399649,MA0107.1;0.107387,MA0108.2;0.540797,MA0109.1;0,MA0111.1;0.234271,MA0113.1;1.06479,MA0114.1;0.339925,MA0115.1;0.929032,MA0116.1;0.10959,MA0117.1;0.732,MA0119.1;0.18693,MA0122.1;0.756889,MA0124.1;0.888592,MA0125.1;0.807083,MA0130.1;0,MA0131.1;0.464307,MA0132.1;0,MA0133.1;0,MA0135.1;0.725055,MA0136.1;0.369468,MA0139.1;0.0564547,MA0140.1;2.38558,MA0141.1;0.197753,MA0142.1;0.514195,MA0143.1;0.414436,MA0144.1;0.0953756,MA0145.1;0.0126924,MA0146.1;0.148267,MA0147.1;0.111828,MA0148.1;0.296708,MA0149.1;0.319221,MA0062.2;0.0599644,MA0035.2;1.56986,MA0039.2;0.00108873,MA0138.2;0.44894,MA0002.2;0.0708857,MA0137.2;0.168782,MA0104.2;0.265556,MA0047.2;0.388882,MA0112.2;0.0113102,MA0065.2;0.0133095,MA0150.1;0.624926,MA0151.1;0,MA0152.1;0.333125,MA0153.1;0.790794,MA0154.1;0.687815,MA0155.1;0.0505475,MA0156.1;0.170442,MA0157.1;0.489002,MA0158.1;0,MA0159.1;0.361202,MA0160.1;0.30953,MA0161.1;0,MA0162.1;0.00136062,MA0163.1;0.00470912,MA0164.1;0.425415,MA0080.2;0.154815,MA0018.2;0.400879,MA0099.2;0.886817,MA0079.2;4.29033e-06,MA0102.2;1.22472,MA0258.1;0.089643,MA0259.1;0.374338,MA0442.1;0}}
|full_id=C614_bone_mesenchymal_basal_mesodermal_Adipocyte_mature_Myoblast
|id=C614
}}

Latest revision as of 11:27, 17 September 2013


Full id: C614_bone_mesenchymal_basal_mesodermal_Adipocyte_mature_Myoblast



Phase1 CAGE Peaks

Hg19::chr10:132684824..132684837,+p@chr10:132684824..132684837
+
Hg19::chr11:24518419..24518445,+p3@LUZP2
Hg19::chr14:102704788..102704801,-p10@MOK
Hg19::chr14:102704806..102704814,-p26@MOK
Hg19::chr14:102704830..102704841,-p25@MOK
Hg19::chr14:36645620..36645634,-p6@ENST00000556013
Hg19::chr14:36645880..36645891,-p7@ENST00000556013
Hg19::chr14:36645917..36645934,-p3@ENST00000556013
Hg19::chr2:170665139..170665155,+p5@SSB
Hg19::chr2:170665157..170665172,+p8@SSB
Hg19::chr2:221311010..221311014,+p@chr2:221311010..221311014
+
Hg19::chr5:121490583..121490596,-p1@ENST00000504829
Hg19::chr7:20784945..20784950,+p@chr7:20784945..20784950
+
Hg19::chr7:68782112..68782118,+p@chr7:68782112..68782118
+


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:0008334histone mRNA metabolic process0.00309078064288237
GO:0006400tRNA modification0.00700576945720005
GO:0000049tRNA binding0.00700576945720005
GO:0006383transcription from RNA polymerase III promoter0.00700576945720005
GO:0003729mRNA binding0.00700576945720005
GO:0009451RNA modification0.00772695160720593
GO:0008033tRNA processing0.0135405628164371
GO:0006399tRNA metabolic process0.0280745908395149
GO:0016071mRNA metabolic process0.0391498881431767



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
receptor cell1.32e-096
sensory epithelial cell1.32e-096
olfactory epithelial cell1.32e-096
Uber Anatomy
Ontology termp-valuen
stroma of bone marrow1.46e-501


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)
MA0003.10.00286173
MA0004.10.275994
MA0006.10.152601
MA0007.10.7221
MA0009.10.695988
MA0014.10.00418733
MA0017.11.02314
MA0019.10.403106
MA0024.10.59663
MA0025.10.824398
MA0027.12.28954
MA0028.10.164086
MA0029.10.614815
MA0030.10.604021
MA0031.10.543644
MA0038.10.363295
MA0040.10.620334
MA0041.10.291389
MA0042.10.264992
MA0043.10.69629
MA0046.10.685589
MA0048.10.0262025
MA0050.10.265714
MA0051.10.944936
MA0052.10.623986
MA0055.10.0207496
MA0056.10
MA0057.10.10396
MA0058.10.200063
MA0059.10.57771
MA0060.10.0773489
MA0061.10.224865
MA0063.10
MA0066.10.363668
MA0067.11.00375
MA0068.10.169955
MA0069.11.6324
MA0070.10.671241
MA0071.10.329767
MA0072.10.666958
MA0073.10.000431279
MA0074.10.358953
MA0076.10.212295
MA0077.10.65962
MA0078.10.447828
MA0081.11.72153
MA0083.10.703169
MA0084.11.18798
MA0087.10.664629
MA0088.10.14098
MA0089.10
MA0090.10.223576
MA0091.10.762163
MA0092.10.691297
MA0093.10.469677
MA0095.10
MA0098.10
MA0100.10.375452
MA0101.10.1571
MA0103.10.146091
MA0105.10.0203556
MA0106.10.399649
MA0107.10.107387
MA0108.20.540797
MA0109.10
MA0111.10.234271
MA0113.11.06479
MA0114.10.339925
MA0115.10.929032
MA0116.10.10959
MA0117.10.732
MA0119.10.18693
MA0122.10.756889
MA0124.10.888592
MA0125.10.807083
MA0130.10
MA0131.10.464307
MA0132.10
MA0133.10
MA0135.10.725055
MA0136.10.369468
MA0139.10.0564547
MA0140.12.38558
MA0141.10.197753
MA0142.10.514195
MA0143.10.414436
MA0144.10.0953756
MA0145.10.0126924
MA0146.10.148267
MA0147.10.111828
MA0148.10.296708
MA0149.10.319221
MA0062.20.0599644
MA0035.21.56986
MA0039.20.00108873
MA0138.20.44894
MA0002.20.0708857
MA0137.20.168782
MA0104.20.265556
MA0047.20.388882
MA0112.20.0113102
MA0065.20.0133095
MA0150.10.624926
MA0151.10
MA0152.10.333125
MA0153.10.790794
MA0154.10.687815
MA0155.10.0505475
MA0156.10.170442
MA0157.10.489002
MA0158.10
MA0159.10.361202
MA0160.10.30953
MA0161.10
MA0162.10.00136062
MA0163.10.00470912
MA0164.10.425415
MA0080.20.154815
MA0018.20.400879
MA0099.20.886817
MA0079.24.29033e-06
MA0102.21.22472
MA0258.10.089643
MA0259.10.374338
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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
GATA3#262535.836396362258430.0132868415026020.0469869109027275



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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