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Coexpression cluster:C274: Difference between revisions

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|tf_chipseq_enrich=HSF1#3297;6:20.9732765957447:4.35525014925938e-07:2.08554777780147e-05!PPARGC1A#10891;4:29.791586073501:1.06543821898128e-05:0.000276524110716169
|tf_chipseq_enrich=HSF1#3297;6:20.9732765957447:4.35525014925938e-07:2.08554777780147e-05!PPARGC1A#10891;4:29.791586073501:1.06543821898128e-05:0.000276524110716169
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|tfbs_overrepresentation_for_novel_motifs=0.0639086,0.00101205,0.0598278,1.04632,2.98386,0.670771,0.242587,3.26246,0.78852,0.00500265,0.138628,0.292222,0.0761553,0.230082,1.25254,0.136809,0.179905,0.447649,0.171203,0.130735,0.160046,0.0397923,0.158328,2.447,0.0875587,0.658003,0.106064,0.156373,0.425591,0.145771,0.532638,0.202712,0.103712,0.0789172,0.519009,0.00381228,0.0782022,0.378406,0.259635,0.00492743,0.176124,0.0255071,0.151006,0.0384376,0.00739999,0.199506,0.243786,0.560935,0.363586,0.243845,0.103211,0.256918,0.12497,0.253654,0.366286,0.0655743,0.0428892,0.199019,0.0809447,0.0536056,0.229344,0.070154,0.791579,0.163473,0.266605,0.143999,0.436932,0.759916,0.196165,0.61311,0.243251,1.10543,0.0149039,0.364729,0.00252675,1.32454,0.00586661,0.153778,0.194134,0.40756,2.04789,0.16285,0.0771509,0.0721084,0.868823,4.76079e-05,0.198252,0.33414,0.115837,0.852295,0.515064,0.305295,0.213484,0.364229,0.00762541,0.611523,0.600102,0.678272,0.118145,0.101915,0.0610803,0.209836,0.237959,0.536884,0.84303,0.134809,0.513706,0.226387,0.0873895,0.0332428,0.344113,0.665136,1.1204,0.340172,1.19484,0.025088,0.179211,0.28664,0.439533,2.12088,0.942045,0.367476,0.663196,0.586337,0.569162,0.154209,0.871061,0.216727,0.391733,0.248119,1.49457,0.539947,1.04066,2.61999,0.526085,0.00363064,0.115995,0.359885,0.489984,1.28951,0.901617,0.458761,0.511074,0.672713,0.429326,0.0511417,0.129791,1.13449,0.105656,0.108523,0.053043,1.0613e-06,0.306085,0.0597614,0.245864,0.640362,0.349799,0.0994284,0.0875978,0.0148645,0.457752,1.44671,0.193642,0.185507,7.04815,0.56138,0.702699,0.241125,2.66019e-05
}}
}}

Revision as of 14:00, 26 November 2012


Full id: C274_CD14_Mast_immature_Basophils_mature_vagina_Hepatocyte



Phase1 CAGE Peaks

Hg19::chr10:134775979..134775984,+p@chr10:134775979..134775984
+
Hg19::chr11:63298876..63298880,-p@chr11:63298876..63298880
-
Hg19::chr11:65951241..65951245,-p@chr11:65951241..65951245
-
Hg19::chr12:104356528..104356534,+p@chr12:104356528..104356534
+
Hg19::chr12:1704684..1704694,+p@chr12:1704684..1704694
+
Hg19::chr12:31890320..31890327,-p@chr12:31890320..31890327
-
Hg19::chr12:52427143..52427164,+p@chr12:52427143..52427164
+
Hg19::chr12:7009390..7009406,+p@chr12:7009390..7009406
+
Hg19::chr13:31736341..31736352,+p@chr13:31736341..31736352
+
Hg19::chr13:75902777..75902790,-p@chr13:75902777..75902790
-
Hg19::chr14:65634137..65634143,+p@chr14:65634137..65634143
+
Hg19::chr14:93799634..93799654,-p5@BTBD7
Hg19::chr15:42787452..42787465,+p3@SNAP23
Hg19::chr16:31398258..31398263,+p@chr16:31398258..31398263
+
Hg19::chr17:72267455..72267461,-p@chr17:72267455..72267461
-
Hg19::chr18:77905923..77905938,+p1@LOC100130522
Hg19::chr19:2678248..2678258,-p@chr19:2678248..2678258
-
Hg19::chr19:54828407..54828412,+p@chr19:54828407..54828412
+
Hg19::chr19:7643171..7643177,-p@chr19:7643171..7643177
-
Hg19::chr19:9906796..9906801,-p@chr19:9906796..9906801
-
Hg19::chr1:12207060..12207069,+p@chr1:12207060..12207069
+
Hg19::chr1:173183104..173183105,+p@chr1:173183104..173183105
+
Hg19::chr1:212661739..212661745,-p@chr1:212661739..212661745
-
Hg19::chr20:17891803..17891806,+p@chr20:17891803..17891806
+
Hg19::chr20:2189294..2189298,+p@chr20:2189294..2189298
+
Hg19::chr20:47526947..47526954,-p@chr20:47526947..47526954
-
Hg19::chr20:49087009..49087016,-p@chr20:49087009..49087016
-
Hg19::chr21:45626767..45626771,+p@chr21:45626767..45626771
+
Hg19::chr22:25403779..25403785,+p@chr22:25403779..25403785
+
Hg19::chr2:242786344..242786355,+p5@ENST00000442867
Hg19::chr2:97232612..97232618,+p@chr2:97232612..97232618
+
Hg19::chr3:13493495..13493517,+p@chr3:13493495..13493517
+
Hg19::chr3:171812201..171812209,+p@chr3:171812201..171812209
+
Hg19::chr5:142147544..142147559,-p@chr5:142147544..142147559
-
Hg19::chr5:157026809..157026848,+p@chr5:157026809..157026848
+
Hg19::chr5:172199724..172199762,+p@chr5:172199724..172199762
+
Hg19::chr6:28222032..28222038,-p@chr6:28222032..28222038
-
Hg19::chr6:30755729..30755743,-p@chr6:30755729..30755743
-
Hg19::chr7:102336834..102336841,+p@chr7:102336834..102336841
+
Hg19::chr7:148224682..148224688,-p@chr7:148224682..148224688
-
Hg19::chr7:22867497..22867502,+p@chr7:22867497..22867502
+
Hg19::chr7:76803755..76803761,-p@chr7:76803755..76803761
-
Hg19::chr8:72754636..72754663,-p@chr8:72754636..72754663
-
Hg19::chr8:72754885..72754889,+p2@LOC100132891
Hg19::chr9:134516035..134516082,+p@chr9:134516035..134516082
+
Hg19::chr9:34986960..34986973,+p@chr9:34986960..34986973
+
Hg19::chrX:1441548..1441556,+p@chrX:1441548..1441556
+


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:0006903vesicle targeting0.00871164714386449
GO:0051650establishment of vesicle localization0.00871164714386449
GO:0051648vesicle localization0.00871164714386449
GO:0006892post-Golgi vesicle-mediated transport0.0100167719467249
GO:0051656establishment of organelle localization0.0100167719467249
GO:0051640organelle localization0.0100691349978272
GO:0019717synaptosome0.0100691349978272
GO:0006944membrane fusion0.0100691349978272
GO:0048193Golgi vesicle transport0.0215127152599617



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 monocyte1.54e-11142
CD14-positive, CD16-negative classical monocyte1.54e-11142
defensive cell8.46e-9748
phagocyte8.46e-9748
monopoietic cell3.71e-7659
monocyte3.71e-7659
monoblast3.71e-7659
promonocyte3.71e-7659
myeloid leukocyte1.85e-7472
macrophage dendritic cell progenitor1.71e-7361
myeloid lineage restricted progenitor cell4.49e-7266
granulocyte monocyte progenitor cell6.44e-7167
stuff accumulating cell1.63e-5087
myeloid cell1.23e-47108
common myeloid progenitor1.23e-47108
hematopoietic lineage restricted progenitor cell3.53e-42120
nongranular leukocyte1.62e-41115
leukocyte2.02e-41136
hematopoietic oligopotent progenitor cell5.98e-34161
hematopoietic multipotent progenitor cell5.98e-34161
hematopoietic stem cell2.98e-32168
angioblastic mesenchymal cell2.98e-32168
hematopoietic cell2.89e-30177
mesenchymal cell1.34e-11354
connective tissue cell3.11e-11361
motile cell6.02e-10386
multi fate stem cell2.27e-08427
somatic stem cell3.75e-08433
stem cell7.16e-08441
basophil1.99e-073
Uber Anatomy
Ontology termp-valuen
bone marrow7.32e-6276
bone element6.49e-5782
immune system3.58e-5693
hematopoietic system5.40e-5398
blood island5.40e-5398
skeletal element2.49e-5190
hemolymphoid system1.65e-47108
skeletal system1.36e-45100
musculoskeletal system9.54e-25167
lateral plate mesoderm3.52e-22203
mesoderm7.74e-12315
mesoderm-derived structure7.74e-12315
presumptive mesoderm7.74e-12315
connective tissue9.79e-11371


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
HSF1#3297620.97327659574474.35525014925938e-072.08554777780147e-05
PPARGC1A#10891429.7915860735011.06543821898128e-050.000276524110716169



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

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