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Coexpression cluster:C1577: Difference between revisions

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|tf_chipseq_enrich=FOXA1#3169;3:6.64885184963127:0.00638902516656872:0.0278038001321418!FOXA2#3170;3:14.7782782515991:0.000628919285119448:0.0051727595856505!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0139941225544512!MXI1#4601;3:5.97694297725558:0.00865300488936688:0.032938882404162
|tf_chipseq_enrich=FOXA1#3169;3:6.64885184963127:0.00638902516656872:0.0278038001321418!FOXA2#3170;3:14.7782782515991:0.000628919285119448:0.0051727595856505!MAX#4149;4:5.1620444072057:0.00252630900948518:0.0139941225544512!MXI1#4601;3:5.97694297725558:0.00865300488936688:0.032938882404162
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|tfbs_overrepresentation_for_novel_motifs=1.26722,0.0561813,0.500341,0.654974,0.454983,0.653236,0.733342,0.866061,0.321368,0.106358,0.621241,0.778743,0.752887,0.721271,1.14971,0.478935,0.963929,0.395009,0.784337,0.167776,0.500405,0.121147,0.645033,0.44943,0.549618,0.802434,0.700122,1.55072,0.458349,0.233785,0.598009,1.00172,0.359091,0.27659,0.417272,0.0526856,1.87167,0.654459,1.00769,0.815792,0.415749,0.580638,0.132849,0.451846,0.476793,0.533483,0.734485,0.609718,0.124583,0.458489,0.817229,0.746838,0.191745,1.08035,1.2359,0.724351,0.4631,0.689906,0.233662,0.688844,1.04369,0.736968,0.321912,0.935408,0.755773,2.08177,1.32544,1.69665,0.991065,1.53343,0.566575,0.330474,1.05625,1.23387,0.269111,0.255232,0.240727,0.917983,0.987729,0.543014,0.293154,0.934302,0.755403,0.327263,1.18161,0.914416,0.166306,0.228496,0.844289,1.79645,1.41984,1.15413,1.01895,0.96134,0.455791,0.381528,0.28626,1.06255,0.849074,0.211081,0.389604,1.01316,1.05685,0.967698,0.88799,0.616433,0.951411,0.717647,0.549347,0.437618,0.512457,1.05402,0.494368,0.631235,1.37132,0.412056,0.285668,2.47721,0.897476,0.370186,1.22546,0.841768,0.650322,0.767198,1.48307,0.918767,0.72668,1.02407,1.2687,0.382577,1.15483,0.601055,1.28328,0.763715,1.43285,0.221105,0.591636,0.643339,1.38998,2.25246,1.84906,1.35224,0.728494,1.05895,2.06113,0.680988,0.87256,2.09294,0.577088,0.363423,0.177807,1.29319,1.15522,0.312599,0.736459,1.56426,0.827475,1.12014,0.54968,0.518696,1.35101,1.13636,0.98692,0.522159,0.906429,0.754576,0.35004,0.731946,0.0214572
}}
}}

Revision as of 14:58, 26 November 2012


Full id: C1577_Mast_CD4_CD34_CD8_Natural_CD14_immature



Phase1 CAGE Peaks

Hg19::chr10:3916381..3916422,+p@chr10:3916381..3916422
+
Hg19::chr11:66384629..66384643,+p6@RBM14
Hg19::chr3:107941436..107941490,+p@chr3:107941436..107941490
+
Hg19::chr3:32543733..32543758,+p@chr3:32543733..32543758
+
Hg19::chr5:672925..672969,-p@chr5:672925..672969
-


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
leukocyte4.12e-43136
hematopoietic lineage restricted progenitor cell1.24e-35120
hematopoietic stem cell5.29e-35168
angioblastic mesenchymal cell5.29e-35168
hematopoietic cell2.20e-33177
hematopoietic oligopotent progenitor cell6.46e-32161
hematopoietic multipotent progenitor cell6.46e-32161
nongranular leukocyte4.00e-31115
lymphoid lineage restricted progenitor cell9.49e-2152
nucleate cell9.75e-2155
lymphocyte3.41e-2053
common lymphoid progenitor3.41e-2053
myeloid leukocyte2.53e-1572
granulocyte monocyte progenitor cell3.04e-1467
T cell6.56e-1425
pro-T cell6.56e-1425
mature alpha-beta T cell9.55e-1418
alpha-beta T cell9.55e-1418
immature T cell9.55e-1418
mature T cell9.55e-1418
immature alpha-beta T cell9.55e-1418
myeloid lineage restricted progenitor cell3.14e-1366
myeloid cell3.55e-13108
common myeloid progenitor3.55e-13108
classical monocyte3.63e-1342
CD14-positive, CD16-negative classical monocyte3.63e-1342
CD4-positive, alpha-beta T cell1.64e-126
intermediate monocyte3.27e-129
CD14-positive, CD16-positive monocyte3.27e-129
macrophage dendritic cell progenitor4.47e-1161
defensive cell8.40e-1148
phagocyte8.40e-1148
mesenchymal cell6.75e-10354
monopoietic cell2.20e-0959
monocyte2.20e-0959
monoblast2.20e-0959
promonocyte2.20e-0959
connective tissue cell2.37e-09361
Langerhans cell5.77e-095
motile cell8.76e-09386
natural killer cell3.53e-073
pro-NK cell3.53e-073
naive T cell7.23e-073
basophil7.66e-073
histamine secreting cell9.33e-075
biogenic amine secreting cell9.33e-075
granulocytopoietic cell9.33e-075
mast cell9.33e-075
mast cell progenitor9.33e-075
basophil mast progenitor cell9.33e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.51e-1598
blood island2.51e-1598
hemolymphoid system5.89e-13108
bone marrow9.38e-1376
immune system1.71e-1193
bone element3.08e-1182
skeletal element1.50e-0990
connective tissue1.29e-08371
skeletal system7.42e-08100


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
FOXA1#316936.648851849631270.006389025166568720.0278038001321418
FOXA2#3170314.77827825159910.0006289192851194480.0051727595856505
MAX#414945.16204440720570.002526309009485180.0139941225544512
MXI1#460135.976942977255580.008653004889366880.032938882404162



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.