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Coexpression cluster:C432: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0002371!4.03e-37!76;UBERON:0001474!2.42e-34!82;UBERON:0004765!3.32e-31!90;UBERON:0002405!3.64e-30!93;UBERON:0002390!1.42e-28!98;UBERON:0003061!1.42e-28!98;UBERON:0001434!5.58e-28!100;UBERON:0002193!7.99e-26!108;UBERON:0002204!3.08e-16!167;UBERON:0003081!4.26e-13!203;UBERON:0000926!7.36e-08!315;UBERON:0004120!7.36e-08!315;UBERON:0006603!7.36e-08!315
|ontology_enrichment_uberon=UBERON:0002371!4.03e-37!76;UBERON:0001474!2.42e-34!82;UBERON:0004765!3.32e-31!90;UBERON:0002405!3.64e-30!93;UBERON:0002390!1.42e-28!98;UBERON:0003061!1.42e-28!98;UBERON:0001434!5.58e-28!100;UBERON:0002193!7.99e-26!108;UBERON:0002204!3.08e-16!167;UBERON:0003081!4.26e-13!203;UBERON:0000926!7.36e-08!315;UBERON:0004120!7.36e-08!315;UBERON:0006603!7.36e-08!315
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|tfbs_overrepresentation_for_novel_motifs=0.086801,0.0156627,0.0831821,0.495534,0.495107,0.954252,0.21518,0.464803,0.241904,0.0364691,0.446032,0.68884,0.168902,0.207164,0.2271,0.0738451,0.386278,0.374077,0.0730138,0.0487616,1.48582,0.0191101,0.159229,0.483467,0.106647,0.263074,0.137425,0.477404,0.0653771,0.242092,0.819121,0.416977,0.0319501,0.172492,0.0500279,0.0305241,0.0488212,0.16489,0.646736,0.210403,1.12158,0.122756,0.135175,0.0628082,0.0193474,0.0986693,0.215945,0.138738,0.21147,0.232836,0.752093,0.224271,0.157142,0.482679,0.61862,0.209199,0.512266,0.186863,0.115345,0.18619,0.451758,0.217609,0.242804,0.363534,0.230363,0.33576,0.699678,1.04962,0.408258,0.893579,0.11533,0.257112,0.00364282,0.616804,0.0126142,0.290509,0.257418,0.349828,0.405538,0.103348,0.383223,0.362659,1.21493,0.251709,0.570388,0.000737971,0.113157,0.109156,0.293613,1.14619,0.786844,0.546282,0.43117,0.321513,0.0643605,0.348406,0.186686,0.467605,0.297172,0.030006,0.36371,1.09109,0.462798,1.01029,0.326595,0.142545,0.376249,1.75235,0.346108,0.057369,0.0887009,0.460417,0.275626,0.151086,0.741849,0.718696,0.00132745,0.131498,0.333893,0.0350599,0.60929,1.4438,0.162396,0.238235,0.846043,0.350442,0.605496,0.435409,1.56193,0.350382,0.546896,0.133891,0.66129,1.23665,0.798972,0.00638711,0.128702,0.15822,0.759101,1.59408,1.19737,0.724259,1.14509,0.464565,0.327989,0.534721,0.314828,1.43649,0.120862,0.0331453,0.0570933,0.0218177,0.547236,0.0910114,0.217268,0.922839,0.281215,0.058186,0.346552,0.0916077,0.723128,1.31504,0.404879,0.0932398,0.903283,0.649817,0.029532,0.6138,0.000815147
}}
}}

Revision as of 14:12, 26 November 2012


Full id: C432_CD14_choriocarcinoma_Peripheral_CD34_Mast_Fibroblast_granulocyte



Phase1 CAGE Peaks

Hg19::chr12:12605663..12605676,+p@chr12:12605663..12605676
+
Hg19::chr12:12605695..12605708,+p@chr12:12605695..12605708
+
Hg19::chr12:82194544..82194548,+p@chr12:82194544..82194548
+
Hg19::chr12:82204256..82204263,+p@chr12:82204256..82204263
+
Hg19::chr16:86018820..86018823,-p@chr16:86018820..86018823
-
Hg19::chr18:3625092..3625104,+p@chr18:3625092..3625104
+
Hg19::chr1:236021384..236021389,+p@chr1:236021384..236021389
+
Hg19::chr1:94344048..94344055,-p@chr1:94344048..94344055
-
Hg19::chr3:171528432..171528445,-p5@PLD1
Hg19::chr3:197798851..197798882,-p@chr3:197798851..197798882
-
Hg19::chr3:197820053..197820077,-p@chr3:197820053..197820077
-
Hg19::chr5:171837860..171837871,+p@chr5:171837860..171837871
+
Hg19::chr5:65030399..65030409,+p@chr5:65030399..65030409
+
Hg19::chr5:77581386..77581396,+p@chr5:77581386..77581396
+
Hg19::chr5:77583788..77583798,-p@chr5:77583788..77583798
-
Hg19::chr8:133846294..133846325,+p@chr8:133846294..133846325
+
Hg19::chr8:133847581..133847588,-p@chr8:133847581..133847588
-
Hg19::chr8:133847743..133847756,+p@chr8:133847743..133847756
+
Hg19::chr8:29693127..29693132,-p@chr8:29693127..29693132
-
Hg19::chr8:39801800..39801807,+p@chr8:39801800..39801807
+
Hg19::chr8:39807228..39807234,-p@chr8:39807228..39807234
-
Hg19::chr9:15298766..15298791,+p@chr9:15298766..15298791
+
Hg19::chr9:15306169..15306172,+p@chr9:15306169..15306172
+


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 monocyte4.30e-6942
CD14-positive, CD16-negative classical monocyte4.30e-6942
defensive cell2.62e-6048
phagocyte2.62e-6048
monopoietic cell5.30e-4859
monocyte5.30e-4859
monoblast5.30e-4859
promonocyte5.30e-4859
macrophage dendritic cell progenitor2.06e-4661
myeloid lineage restricted progenitor cell7.44e-4366
granulocyte monocyte progenitor cell3.32e-4267
myeloid leukocyte3.16e-3972
stuff accumulating cell1.06e-3287
myeloid cell7.99e-26108
common myeloid progenitor7.99e-26108
nongranular leukocyte3.52e-24115
hematopoietic lineage restricted progenitor cell4.02e-23120
leukocyte2.98e-20136
hematopoietic oligopotent progenitor cell6.76e-17161
hematopoietic multipotent progenitor cell6.76e-17161
hematopoietic stem cell3.92e-16168
angioblastic mesenchymal cell3.92e-16168
hematopoietic cell3.07e-15177
mesenchymal cell8.46e-07354
Uber Anatomy
Ontology termp-valuen
bone marrow4.03e-3776
bone element2.42e-3482
skeletal element3.32e-3190
immune system3.64e-3093
hematopoietic system1.42e-2898
blood island1.42e-2898
skeletal system5.58e-28100
hemolymphoid system7.99e-26108
musculoskeletal system3.08e-16167
lateral plate mesoderm4.26e-13203
mesoderm7.36e-08315
mesoderm-derived structure7.36e-08315
presumptive mesoderm7.36e-08315


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)

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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.