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Coexpression cluster:C1380: Difference between revisions

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|tf_chipseq_enrich=FOSL1#8061;3:19.8567898581865:0.000301402757252219:0.00311018699384097!JUN#3725;5:10.4273576602803:1.82465747415735e-05:0.000415265639449813!JUND#3727;4:4.66310929458068:0.00491764340826023:0.0229878148740171!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296016184871692
|tf_chipseq_enrich=FOSL1#8061;3:19.8567898581865:0.000301402757252219:0.00311018699384097!JUN#3725;5:10.4273576602803:1.82465747415735e-05:0.000415265639449813!JUND#3727;4:4.66310929458068:0.00491764340826023:0.0229878148740171!USF1#7391;4:4.24099951813864:0.00700536775082942:0.0296016184871692
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|tfbs_overrepresentation_for_novel_motifs=0.44418,1.82196,0.436508,0.58616,0.393082,0.584466,0.662701,0.269608,0.736703,0.075749,0.553339,0.707204,0.223349,0.650887,0.391663,0.415981,0.889639,0.336106,0.664996,0.402028,0.436569,0.29639,0.576478,0.387783,0.483957,0.730467,0.202389,0.574247,0.396295,0.186644,0.530785,0.92701,0.302275,0.225641,0.35719,1.30732,0.35388,0.585658,0.878269,0.248856,0.355745,0.513952,0.664116,0.390088,0.636689,0.468392,0.66382,0.542147,1.56014,1.02586,0.745008,0.675919,0.455399,1.00488,1.15929,0.653901,0.400834,0.62023,0.547548,0.619193,0.968558,0.666252,0.737866,0.861462,0.684675,0.826413,1.24834,1.61834,0.916468,1.45553,0.500342,0.275507,0.146905,1.15727,0.218784,0.594475,1.07049,0.84426,0.913168,2.08653,0.240887,0.86037,0.684313,0.272514,1.10535,0.406668,0.398737,0.536262,0.771626,1.71797,1.34233,1.07807,0.94406,0.83374,0.393853,0.32338,0.661488,0.987239,0.776336,0.166235,0.330999,0.938327,0.981588,0.893363,0.814675,0.548668,0.877269,0.647343,0.483695,0.376529,1.13818,0.978783,0.430775,1.38333,1.29401,0.928633,0.0577227,0.529546,0.824029,0.312699,1.14892,0.769145,0.581628,0.695878,1.40534,0.845034,0.656181,0.949126,1.1919,0.866571,1.07876,0.53374,1.20639,0.692462,1.35529,0.175219,0.524606,0.57483,1.31259,2.17352,1.7705,1.27501,0.657956,0.983666,0.816466,0.611524,0.799467,2.01411,0.510514,0.306342,0.424432,0.0926553,1.07915,0.717973,0.665754,1.48627,0.755083,0.378604,0.484017,0.454152,1.27379,1.06043,0.912368,0.457485,0.83286,0.683502,0.29379,0.661335,0.0564726
}}
}}

Revision as of 14:51, 26 November 2012


Full id: C1380_Mast_CD14_Basophils_embryonic_pineal_CD133_CD4



Phase1 CAGE Peaks

Hg19::chr13:31735232..31735251,-p@chr13:31735232..31735251
-
Hg19::chr16:29302794..29302807,+p@chr16:29302794..29302807
+
Hg19::chr17:40517403..40517408,+p@chr17:40517403..40517408
+
Hg19::chr4:77928601..77928612,-p@chr4:77928601..77928612
-
Hg19::chr8:581156..581176,+p@chr8:581156..581176
+
Hg19::chr9:130624985..130624989,+p@chr9:130624985..130624989
+


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><br>


Cell Type
Ontology termp-valuen
classical monocyte1.63e-4442
CD14-positive, CD16-negative classical monocyte1.63e-4442
myeloid leukocyte2.14e-4272
defensive cell1.53e-3848
phagocyte1.53e-3848
myeloid lineage restricted progenitor cell5.54e-3866
granulocyte monocyte progenitor cell2.28e-3767
monopoietic cell3.55e-3059
monocyte3.55e-3059
monoblast3.55e-3059
promonocyte3.55e-3059
leukocyte7.26e-30136
macrophage dendritic cell progenitor4.27e-2961
myeloid cell4.86e-27108
common myeloid progenitor4.86e-27108
hematopoietic lineage restricted progenitor cell3.26e-26120
hematopoietic stem cell2.35e-23168
angioblastic mesenchymal cell2.35e-23168
hematopoietic oligopotent progenitor cell1.70e-22161
hematopoietic multipotent progenitor cell1.70e-22161
nongranular leukocyte3.16e-22115
hematopoietic cell6.07e-22177
natural killer cell1.15e-203
pro-NK cell1.15e-203
stuff accumulating cell8.82e-2087
histamine secreting cell8.93e-145
biogenic amine secreting cell8.93e-145
granulocytopoietic cell8.93e-145
mast cell8.93e-145
mast cell progenitor8.93e-145
basophil mast progenitor cell8.93e-145
basophil1.78e-103
mesenchymal cell1.17e-08354
connective tissue cell2.14e-08361
endocrine cell7.39e-089
motile cell1.78e-07386
Uber Anatomy
Ontology termp-valuen
bone marrow1.49e-3276
bone element6.34e-3082
hematopoietic system3.98e-2798
blood island3.98e-2798
skeletal element5.90e-2790
immune system5.68e-2693
hemolymphoid system2.85e-24108
skeletal system6.64e-24100
musculoskeletal system8.10e-13167
lateral plate mesoderm4.43e-11203
connective tissue5.75e-09371


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)

{{{tfbs_overrepresentation_jaspar}}}



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
FOSL1#8061319.85678985818650.0003014027572522190.00311018699384097
JUN#3725510.42735766028031.82465747415735e-050.000415265639449813
JUND#372744.663109294580680.004917643408260230.0229878148740171
USF1#739144.240999518138640.007005367750829420.0296016184871692



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.