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Coexpression cluster:C578: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;8:2.85880339897335:0.00268164727109909:0.0147723276199334!E2F1#1869;8:2.61727424793564:0.00478608560856321:0.0224906184419678!EBF1#1879;8:4.75011565150347:7.80369455890836e-05:0.00120225705271844!POLR2A#5430;12:1.71796254124646:0.00885747283887137:0.0336167456144664!TFAP2C#7022;5:3.60307620328674:0.00920612058381016:0.0348071544601437
|tf_chipseq_enrich=CTCF#10664;8:2.85880339897335:0.00268164727109909:0.0147723276199334!E2F1#1869;8:2.61727424793564:0.00478608560856321:0.0224906184419678!EBF1#1879;8:4.75011565150347:7.80369455890836e-05:0.00120225705271844!POLR2A#5430;12:1.71796254124646:0.00885747283887137:0.0336167456144664!TFAP2C#7022;5:3.60307620328674:0.00920612058381016:0.0348071544601437
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|tfbs_overrepresentation_for_novel_motifs=1.57187,0.519727,0.501231,0.277483,0.429786,0.276158,0.338925,0.241,0.237344,0.507384,0.252096,0.3759,0.177832,0.329255,1.36411,0.467196,0.534852,0.104074,1.15732,0.178501,0.16756,1.17624,0.26993,0.42122,0.200668,1.02394,0.151052,0.739386,0.434999,0.310781,0.235027,0.568576,2.06705,0.405736,0.37247,0.109438,0.740892,0.27709,0.675484,1.22473,0.370199,0.222502,0.118046,0.136946,0.565712,0.554944,0.339845,0.243586,0.223066,0.435216,0.407934,0.923261,0.428224,0.639823,0.784252,0.331716,0.143846,0.821863,0.896459,0.303639,0.606437,0.90555,0.238061,0.509653,0.357077,0.478604,0.869007,1.22829,0.559029,1.06908,1.1473,0.249409,1.01512,0.782342,0.388726,0.999692,0.139392,0.494371,1.36852,0.570606,0.201166,0.50868,0.356776,0.245133,0.733386,0.929166,0.872841,0.550078,1.10067,1.32629,0.95934,0.70782,0.584068,0.299574,0.850013,0.320157,0.192618,0.623577,0.434875,0.491693,0.10113,0.578851,0.618385,0.538198,0.468285,0.694065,0.523764,0.326366,0.20048,1.3044,0.520729,0.61581,0.163638,1.32564,0.912801,0.736459,1.39711,0.660476,0.476505,0.304012,0.77444,0.428661,0.273941,0.366411,1.02031,0.495057,0.33358,0.588683,0.815183,0.661484,0.708473,0.237246,0.828971,0.363559,0.971853,0.283882,0.651842,0.268649,0.930667,1.77777,1.3781,0.894557,0.335034,0.620293,1.18491,0.297516,0.454976,1.61933,0.627312,1.02878,0.943814,1.23015,0.708834,0.489782,0.341434,1.09904,0.41656,0.129698,0.200711,0.530833,0.893382,0.691354,0.555323,1.02668,0.48429,0.356103,0.0806293,0.337803,2.22883
}}
}}

Revision as of 14:19, 26 November 2012


Full id: C578_CD34_Natural_CD8_CD4_CD133_Basophils_CD14



Phase1 CAGE Peaks

Hg19::chr10:12390958..12390973,-p@chr10:12390958..12390973
-
Hg19::chr12:76952682..76952690,-p@chr12:76952682..76952690
-
Hg19::chr13:101326316..101326335,+p@chr13:101326316..101326335
+
Hg19::chr14:105760706..105760717,-p@chr14:105760706..105760717
-
Hg19::chr14:105760904..105760918,+p@chr14:105760904..105760918
+
Hg19::chr15:52970999..52971015,+p@chr15:52970999..52971015
+
Hg19::chr15:52971052..52971073,+p@chr15:52971052..52971073
+
Hg19::chr19:33865006..33865017,-p@chr19:33865006..33865017
-
Hg19::chr1:221916028..221916038,+p@chr1:221916028..221916038
+
Hg19::chr2:122457110..122457118,-p@chr2:122457110..122457118
-
Hg19::chr2:28571261..28571277,+p@chr2:28571261..28571277
+
Hg19::chr6:16762361..16762374,-p@chr6:16762361..16762374
-
Hg19::chr6:34205792..34205795,-p@chr6:34205792..34205795
-
Hg19::chr7:141401439..141401452,+p@chr7:141401439..141401452
+
Hg19::chr8:145013517..145013546,+p@chr8:145013517..145013546
+


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
leukocyte2.90e-30136
hematopoietic stem cell4.50e-27168
angioblastic mesenchymal cell4.50e-27168
hematopoietic cell3.58e-25177
CD4-positive, alpha-beta T cell3.82e-216
hematopoietic oligopotent progenitor cell1.33e-19161
hematopoietic multipotent progenitor cell1.33e-19161
hematopoietic lineage restricted progenitor cell2.83e-19120
nongranular leukocyte6.71e-19115
mature alpha-beta T cell6.61e-1818
alpha-beta T cell6.61e-1818
immature T cell6.61e-1818
mature T cell6.61e-1818
immature alpha-beta T cell6.61e-1818
lymphoid lineage restricted progenitor cell1.40e-1552
lymphocyte3.32e-1553
common lymphoid progenitor3.32e-1553
nucleate cell1.70e-1455
T cell2.74e-1225
pro-T cell2.74e-1225
natural killer cell4.80e-123
pro-NK cell4.80e-123
basophil3.08e-113
naive T cell4.05e-113
plasmacytoid dendritic cell7.21e-113
single nucleate cell1.11e-103
mononuclear cell1.11e-103
myeloid leukocyte5.30e-0972
regulatory T cell9.03e-082
CD4-positive, CD25-positive, alpha-beta regulatory T cell9.03e-082
naive regulatory T cell9.03e-082
mesenchymal cell1.45e-07354
connective tissue cell3.12e-07361
myeloid cell3.78e-07108
common myeloid progenitor3.78e-07108
granulocyte4.35e-078
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.32e-0998
blood island2.32e-0998
hemolymphoid system4.58e-08108
thymus8.56e-084
hemolymphoid system gland8.56e-084
thymic region8.56e-084
pharyngeal gland8.56e-084
thymus primordium8.56e-084
immune system5.97e-0793
connective tissue8.80e-07371


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
CTCF#1066482.858803398973350.002681647271099090.0147723276199334
E2F1#186982.617274247935640.004786085608563210.0224906184419678
EBF1#187984.750115651503477.80369455890836e-050.00120225705271844
POLR2A#5430121.717962541246460.008857472838871370.0336167456144664
TFAP2C#702253.603076203286740.009206120583810160.0348071544601437



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.