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Coexpression cluster:C822: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.280498,0.101185,0.273994,0.404877,0.237701,0.403356,0.474413,0.855419,0.138703,0.0921938,0.980041,1.28238,0.107365,0.46359,0.666154,0.256724,0.68716,0.191625,0.748636,0.400542,0.752779,0.805814,0.396189,0.658697,0.314616,0.537051,0.0930454,0.39419,0.675066,0.281506,0.355553,1.71747,0.165252,0.352585,0.600053,0.359459,0.20579,0.404426,1.04488,0.125439,0.207288,0.340749,0.127662,0.235234,0.00743678,0.301189,1.19689,0.958158,0.116302,0.240465,0.550604,0.486559,0.214602,0.797754,0.947672,0.466348,1.26794,0.435652,0.281305,0.434711,0.762758,0.477672,0.139078,0.660336,0.494624,1.51801,1.0348,1.4,0.712787,1.2388,0.328852,0.874121,0.0579262,0.945703,0.104203,0.0955465,0.292851,0.644006,0.709631,0.309107,1.24887,0.659298,0.49429,1.39374,0.89511,0.0102458,0.175904,1.44963,0.575506,1.4989,1.12715,0.868602,0.739223,0.509773,0.238337,0.18161,0.743843,0.780743,0.579925,0.524614,0.550108,0.733724,0.775299,0.690713,0.616014,0.37138,0.675372,0.460348,1.52535,0.22412,0.283874,0.772599,0.269151,0.384185,1.07963,0.204477,0.0648813,0.354459,0.624851,0.173291,0.937551,0.57318,1.03543,0.504966,1.18924,0.644741,0.468435,0.744085,0.979528,0.182384,0.869279,0.358161,0.993705,0.50181,1.13991,0.260985,0.9239,1.02211,1.09788,1.95265,1.55112,1.06096,0.470062,0.777301,0.617705,0.42776,0.601672,1.79367,0.337738,0.168379,0.429078,0.0287097,0.869654,0.414185,0.477214,1.26919,0.560015,0.225815,0.314669,0.28899,1.05976,0.851493,4.10545,0.291837,0.633206,0.493542,0.158769,0.473159,0.02648
|tfbs_overrepresentation_jaspar=MA0003.1;0.000221536,MA0004.1;0.380329,MA0006.1;0.236135,MA0007.1;0.363007,MA0009.1;0.828613,MA0014.1;0.15363,MA0017.1;0.270554,MA0019.1;0.520264,MA0024.1;0.725404,MA0025.1;0.960689,MA0027.1;2.43535,MA0028.1;0.697761,MA0029.1;0.744375,MA0030.1;0.733118,MA0031.1;0.669876,MA0038.1;0.477043,MA0040.1;0.750125,MA0041.1;0.397617,MA0042.1;0.367902,MA0043.1;0.828925,MA0046.1;0.817858,MA0048.1;0.220931,MA0050.1;0.368721,MA0051.1;1.19169,MA0052.1;0.753928,MA0055.1;0.174262,MA0056.1;0,MA0057.1;0.211138,MA0058.1;0.293055,MA0059.1;0.79343,MA0060.1;0.138988,MA0061.1;0.118318,MA0063.1;0,MA0066.1;0.477449,MA0067.1;1.1435,MA0068.1;0.0911063,MA0069.1;0.814052,MA0070.1;0.803003,MA0071.1;0.440254,MA0072.1;0.798564,MA0073.1;1.11021e-05,MA0074.1;0.4723,MA0076.1;0.828432,MA0077.1;0.790956,MA0078.1;0.568317,MA0081.1;0.292043,MA0083.1;0.836033,MA0084.1;1.32998,MA0087.1;0.79615,MA0088.1;0.126492,MA0089.1;0,MA0090.1;0.320494,MA0091.1;0.382762,MA0092.1;0.347826,MA0093.1;0.238771,MA0095.1;0,MA0098.1;0,MA0100.1;1.2287,MA0101.1;0.241637,MA0103.1;0.228129,MA0105.1;0.0508589,MA0106.1;0.516528,MA0107.1;0.179177,MA0108.2;0.666881,MA0109.1;0,MA0111.1;0.33284,MA0113.1;0.532314,MA0114.1;0.51954,MA0115.1;1.06753,MA0116.1;0.182037,MA0117.1;0.865782,MA0119.1;0.277531,MA0122.1;0.891407,MA0124.1;1.0263,MA0125.1;0.942948,MA0130.1;0,MA0131.1;1.43152,MA0132.1;0,MA0133.1;0,MA0135.1;0.858623,MA0136.1;0.483775,MA0139.1;0.716757,MA0140.1;0.437738,MA0141.1;0.290336,MA0142.1;0.638837,MA0143.1;0.532484,MA0144.1;1.51733,MA0145.1;0.14293,MA0146.1;0.00275056,MA0147.1;0.184931,MA0148.1;0.403564,MA0149.1;0.428597,MA0062.2;0.114378,MA0035.2;0.437071,MA0039.2;0.0109452,MA0138.2;1.39695,MA0002.2;0.129981,MA0137.2;0.255808,MA0104.2;0.138396,MA0047.2;0.504873,MA0112.2;0.313961,MA0065.2;0.0371828,MA0150.1;0.845871,MA0151.1;0,MA0152.1;0.443956,MA0153.1;0.926242,MA0154.1;1.12157,MA0155.1;0.12484,MA0156.1;0.257809,MA0157.1;0.612166,MA0158.1;0,MA0159.1;0.185458,MA0160.1;0.417847,MA0161.1;0,MA0162.1;0.00711618,MA0163.1;0.00405048,MA0164.1;0.544294,MA0080.2;0.671553,MA0018.2;0.517858,MA0099.2;0.444294,MA0079.2;6.65357e-08,MA0102.2;1.36707,MA0258.1;0.919347,MA0259.1;0.191914,MA0442.1;0
}}
}}

Revision as of 19:28, 22 January 2013


Full id: C822_myelodysplastic_acute_Macrophage_Monocytederived_CD14_biphenotypic_Hodgkin



Phase1 CAGE Peaks

Hg19::chr13:105490048..105490074,-p@chr13:105490048..105490074
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Hg19::chr17:56347811..56347816,-p@chr17:56347811..56347816
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Hg19::chr3:183596040..183596055,-p@chr3:183596040..183596055
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Hg19::chr3:183596069..183596083,-p@chr3:183596069..183596083
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Hg19::chr3:183598068..183598079,-p@chr3:183598068..183598079
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Hg19::chr3:183598086..183598109,-p@chr3:183598086..183598109
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Hg19::chr4:26276979..26276986,-p@chr4:26276979..26276986
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Hg19::chr4:26277004..26277023,-p@chr4:26277004..26277023
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Hg19::chr4:26277042..26277057,-p@chr4:26277042..26277057
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Hg19::chr5:177904789..177904800,+p@chr5:177904789..177904800
+


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

No GOStat results

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>

Cell Type
Ontology termp-valuen
myeloid cell1.30e-34108
common myeloid progenitor1.30e-34108
hematopoietic oligopotent progenitor cell1.53e-21161
hematopoietic multipotent progenitor cell1.53e-21161
hematopoietic stem cell2.00e-20168
angioblastic mesenchymal cell2.00e-20168
hematopoietic cell4.03e-19177
myeloid leukocyte2.43e-1772
monopoietic cell1.81e-1659
monocyte1.81e-1659
monoblast1.81e-1659
promonocyte1.81e-1659
macrophage dendritic cell progenitor7.61e-1661
myeloid lineage restricted progenitor cell1.89e-1466
granulocyte monocyte progenitor cell3.39e-1467
immature conventional dendritic cell9.08e-105
common dendritic progenitor9.08e-105
basophil1.02e-083
adult endothelial progenitor cell1.10e-083
leukocyte1.02e-07136
nongranular leukocyte3.54e-07115
mesenchymal cell7.05e-07354
hematopoietic lineage restricted progenitor cell9.02e-07120
Uber Anatomy
Ontology termp-valuen
immune system1.00e-1293
bone marrow3.31e-1276
hematopoietic system6.45e-1298
blood island6.45e-1298
bone element4.03e-1182
hemolymphoid system1.60e-10108
skeletal element6.72e-1090
spleen1.02e-083
gastrointestinal system mesentery1.02e-083
stomach region1.02e-083
mesentery1.02e-083
gastrointestinal system serosa1.02e-083
mesentery of stomach1.02e-083
gut mesentery1.02e-083
dorsal mesentery1.02e-083
dorsal mesogastrium1.02e-083
peritoneal cavity1.02e-083
spleen primordium1.02e-083
skeletal system1.20e-08100
dura mater7.40e-071
future meninx7.40e-071
ectomeninx7.40e-071
future dura mater7.40e-071
Disease
Ontology termp-valuen
myeloid leukemia2.19e-3531
leukemia1.56e-2739
hematologic cancer2.26e-2051
immune system cancer2.26e-2051
syndrome9.91e-081


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)
MA0003.10.000221536
MA0004.10.380329
MA0006.10.236135
MA0007.10.363007
MA0009.10.828613
MA0014.10.15363
MA0017.10.270554
MA0019.10.520264
MA0024.10.725404
MA0025.10.960689
MA0027.12.43535
MA0028.10.697761
MA0029.10.744375
MA0030.10.733118
MA0031.10.669876
MA0038.10.477043
MA0040.10.750125
MA0041.10.397617
MA0042.10.367902
MA0043.10.828925
MA0046.10.817858
MA0048.10.220931
MA0050.10.368721
MA0051.11.19169
MA0052.10.753928
MA0055.10.174262
MA0056.10
MA0057.10.211138
MA0058.10.293055
MA0059.10.79343
MA0060.10.138988
MA0061.10.118318
MA0063.10
MA0066.10.477449
MA0067.11.1435
MA0068.10.0911063
MA0069.10.814052
MA0070.10.803003
MA0071.10.440254
MA0072.10.798564
MA0073.11.11021e-05
MA0074.10.4723
MA0076.10.828432
MA0077.10.790956
MA0078.10.568317
MA0081.10.292043
MA0083.10.836033
MA0084.11.32998
MA0087.10.79615
MA0088.10.126492
MA0089.10
MA0090.10.320494
MA0091.10.382762
MA0092.10.347826
MA0093.10.238771
MA0095.10
MA0098.10
MA0100.11.2287
MA0101.10.241637
MA0103.10.228129
MA0105.10.0508589
MA0106.10.516528
MA0107.10.179177
MA0108.20.666881
MA0109.10
MA0111.10.33284
MA0113.10.532314
MA0114.10.51954
MA0115.11.06753
MA0116.10.182037
MA0117.10.865782
MA0119.10.277531
MA0122.10.891407
MA0124.11.0263
MA0125.10.942948
MA0130.10
MA0131.11.43152
MA0132.10
MA0133.10
MA0135.10.858623
MA0136.10.483775
MA0139.10.716757
MA0140.10.437738
MA0141.10.290336
MA0142.10.638837
MA0143.10.532484
MA0144.11.51733
MA0145.10.14293
MA0146.10.00275056
MA0147.10.184931
MA0148.10.403564
MA0149.10.428597
MA0062.20.114378
MA0035.20.437071
MA0039.20.0109452
MA0138.21.39695
MA0002.20.129981
MA0137.20.255808
MA0104.20.138396
MA0047.20.504873
MA0112.20.313961
MA0065.20.0371828
MA0150.10.845871
MA0151.10
MA0152.10.443956
MA0153.10.926242
MA0154.11.12157
MA0155.10.12484
MA0156.10.257809
MA0157.10.612166
MA0158.10
MA0159.10.185458
MA0160.10.417847
MA0161.10
MA0162.10.00711618
MA0163.10.00405048
MA0164.10.544294
MA0080.20.671553
MA0018.20.517858
MA0099.20.444294
MA0079.26.65357e-08
MA0102.21.36707
MA0258.10.919347
MA0259.10.191914
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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