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Coexpression cluster:C1852: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;2:11.3477820414428:0.0115705693374132:0.0422893680150515!CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319583674041837!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121200251441179!GTF2F1#2962;3:7.64379652605459:0.0042841549641205:0.0203471059707949!JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109364023575858!MEF2A#4205;4:14.9945847277152:3.876195075647e-05:0.000728235181697242!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252460235798799!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00239172676047573!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542672252823319!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000574812312944367!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135454497584577!TBP#6908;5:3.70677068709639:0.00142875510672112:0.0091939466784256!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298474574671828
|tf_chipseq_enrich=BCL11A#53335;2:11.3477820414428:0.0115705693374132:0.0422893680150515!CHD2#1106;3:6.20641370047011:0.00777455012627559:0.0319583674041837!EP300#2033;4:5.41915338097856:0.0020938692794389:0.0121200251441179!GTF2F1#2962;3:7.64379652605459:0.0042841549641205:0.0203471059707949!JUND#3727;4:5.59573115349682:0.00184959330175546:0.0109364023575858!MEF2A#4205;4:14.9945847277152:3.876195075647e-05:0.000728235181697242!MEF2C#4208;2:16.5245417970496:0.00557985007798205:0.0252460235798799!NFKB1#4790;5:5.48806342419384:0.000200816284746232:0.00239172676047573!POU2F2#5452;4:7.28489924619402:0.000663122328874386:0.00542672252823319!SPI1#6688;5:8.20432350852273:2.68916109982495e-05:0.000574812312944367!TAF1#6872;5:3.34304628574529:0.00239460009087031:0.0135454497584577!TBP#6908;5:3.70677068709639:0.00142875510672112:0.0091939466784256!YY1#7528;4:3.92893659988308:0.00719386626991762:0.0298474574671828
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|tfbs_overrepresentation_for_novel_motifs=0.508327,0.452433,0.500341,0.654974,0.454983,0.653236,0.733342,0.324142,0.321368,0.345702,0.621241,0.778743,0.274093,0.721271,0.453496,0.478935,0.963929,0.395009,0.287891,0.501863,0.500405,0.384437,1.55551,1.14094,0.549618,0.802434,0.25115,0.642741,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,1.62925,0.413782,0.654459,0.388123,2.25858,0.415749,0.580638,0.414516,0.451846,0.0606304,0.533483,0.734485,0.609718,0.393318,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,0.899893,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,0.189341,1.23387,0.269111,0.709554,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.251545,7.40739,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,1.49565,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,0.596731,0.897476,0.370186,1.22546,0.841768,1.56655,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,2.60032,0.601055,2.85991,0.763715,1.43285,1.18046,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,0.889806,0.680988,0.87256,2.09294,1.41294,0.363423,0.177807,1.29319,1.15522,0.312599,1.74559,1.56426,0.827475,0.439798,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.443702
}}
}}

Revision as of 15:09, 26 November 2012


Full id: C1852_Neutrophils_CD19_CD4_Peripheral_Eosinophils_Natural_CD8



Phase1 CAGE Peaks

Hg19::chr1:227127664..227127698,-p@chr1:227127664..227127698
-
Hg19::chr1:40840182..40840198,-p@chr1:40840182..40840198
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Hg19::chr1:40840233..40840259,-p@chr1:40840233..40840259
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Hg19::chr1:40851288..40851322,-p@chr1:40851288..40851322
-
Hg19::chr1:40851848..40851881,+p@chr1:40851848..40851881
+


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
leukocyte4.18e-78136
hematopoietic stem cell3.34e-69168
angioblastic mesenchymal cell3.34e-69168
hematopoietic cell1.16e-67177
hematopoietic oligopotent progenitor cell9.11e-64161
hematopoietic multipotent progenitor cell9.11e-64161
nongranular leukocyte1.37e-61115
hematopoietic lineage restricted progenitor cell1.92e-59120
lymphocyte3.74e-4253
common lymphoid progenitor3.74e-4253
lymphoid lineage restricted progenitor cell1.42e-4152
nucleate cell6.38e-4055
myeloid leukocyte2.76e-2672
myeloid cell7.01e-24108
common myeloid progenitor7.01e-24108
T cell3.92e-2125
pro-T cell3.92e-2125
mature alpha-beta T cell1.47e-2018
alpha-beta T cell1.47e-2018
immature T cell1.47e-2018
mature T cell1.47e-2018
immature alpha-beta T cell1.47e-2018
classical monocyte2.03e-2042
CD14-positive, CD16-negative classical monocyte2.03e-2042
granulocyte monocyte progenitor cell4.18e-2067
macrophage dendritic cell progenitor1.93e-1961
myeloid lineage restricted progenitor cell4.91e-1866
monopoietic cell7.69e-1859
monocyte7.69e-1859
monoblast7.69e-1859
promonocyte7.69e-1859
lymphocyte of B lineage9.11e-1824
pro-B cell9.11e-1824
defensive cell1.90e-1648
phagocyte1.90e-1648
mesenchymal cell3.40e-15354
connective tissue cell3.04e-14361
B cell1.18e-1314
CD8-positive, alpha-beta T cell4.21e-1311
motile cell2.25e-11386
granulocyte1.57e-108
intermediate monocyte6.31e-109
CD14-positive, CD16-positive monocyte6.31e-109
blood cell1.03e-0811
CD4-positive, alpha-beta T cell1.12e-086
multi fate stem cell1.51e-07427
stem cell4.17e-07441
somatic stem cell4.69e-07433
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.74e-3498
blood island4.74e-3498
hemolymphoid system3.04e-31108
immune system2.34e-2093
bone marrow3.74e-1876
bone element1.49e-1682
blood2.04e-1415
haemolymphatic fluid2.04e-1415
organism substance2.04e-1415
skeletal element8.54e-1490
connective tissue2.10e-13371
skeletal system1.07e-11100
lateral plate mesoderm2.41e-07203


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
BCL11A#53335211.34778204144280.01157056933741320.0422893680150515
CHD2#110636.206413700470110.007774550126275590.0319583674041837
EP300#203345.419153380978560.00209386927943890.0121200251441179
GTF2F1#296237.643796526054590.00428415496412050.0203471059707949
JUND#372745.595731153496820.001849593301755460.0109364023575858
MEF2A#4205414.99458472771523.876195075647e-050.000728235181697242
MEF2C#4208216.52454179704960.005579850077982050.0252460235798799
NFKB1#479055.488063424193840.0002008162847462320.00239172676047573
POU2F2#545247.284899246194020.0006631223288743860.00542672252823319
SPI1#668858.204323508522732.68916109982495e-050.000574812312944367
TAF1#687253.343046285745290.002394600090870310.0135454497584577
TBP#690853.706770687096390.001428755106721120.0091939466784256
YY1#752843.928936599883080.007193866269917620.0298474574671828



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.