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Coexpression cluster:C2334: Difference between revisions

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|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00816438472300254
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00816438472300254
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|tfbs_overrepresentation_for_novel_motifs=0.590005,0.0888524,0.581696,0.741427,0.534346,0.739643,0.821651,0.395818,1.01802,0.151681,0.706765,0.867962,0.341754,0.809319,0.532789,0.559384,1.05593,0.471262,0.356737,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,0.316693,1.72987,0.537869,0.297585,0.682839,1.09415,0.433165,0.344471,0.49475,0.0842336,0.491074,0.740899,0.463978,0.371755,0.493145,0.66492,0.183156,0.53106,0.0946706,0.61613,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,3.13598,1.79268,1.08337,1.62905,0.650393,0.402607,0.248021,1.32819,0.336329,1.54953,0.305238,1.00941,1.08,0.62601,0.362435,1.02594,0.844168,0.399165,1.27559,0.109222,0.221873,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,1.32435,0.456994,0.354969,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,1.22649,0.12452,0.681522,0.988625,1.1313,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,2.78996,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,1.94535,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,0.234974,0.175846,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,1.90479,0.820225,0.156682
}}
}}

Revision as of 15:26, 26 November 2012


Full id: C2334_Neutrophils_Monocytederived_Whole_myeloma_CD14_blood_CD4



Phase1 CAGE Peaks

Hg19::chr15:45010031..45010067,+p@chr15:45010031..45010067
+
Hg19::chr15:45010077..45010108,+p@chr15:45010077..45010108
+
Hg19::chr15:45010168..45010186,+p@chr15:45010168..45010186
+
Hg19::chr15:45010228..45010300,+p@chr15:45010228..45010300
+


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
leukocyte3.11e-42136
nongranular leukocyte6.54e-38115
hematopoietic lineage restricted progenitor cell2.67e-34120
hematopoietic stem cell4.56e-32168
angioblastic mesenchymal cell4.56e-32168
hematopoietic oligopotent progenitor cell1.99e-31161
hematopoietic multipotent progenitor cell1.99e-31161
hematopoietic cell1.68e-30177
myeloid leukocyte1.43e-2872
macrophage dendritic cell progenitor1.32e-2761
monopoietic cell4.06e-2759
monocyte4.06e-2759
monoblast4.06e-2759
promonocyte4.06e-2759
defensive cell1.32e-2648
phagocyte1.32e-2648
granulocyte monocyte progenitor cell9.53e-2567
myeloid lineage restricted progenitor cell1.56e-2366
classical monocyte3.66e-2342
CD14-positive, CD16-negative classical monocyte3.66e-2342
myeloid cell8.39e-20108
common myeloid progenitor8.39e-20108
mesenchymal cell8.35e-13354
connective tissue cell4.83e-12361
lymphocyte7.54e-1153
common lymphoid progenitor7.54e-1153
lymphoid lineage restricted progenitor cell1.43e-1052
nucleate cell1.19e-0955
multi fate stem cell5.23e-09427
somatic stem cell7.19e-08433
mature alpha-beta T cell7.92e-0818
alpha-beta T cell7.92e-0818
immature T cell7.92e-0818
mature T cell7.92e-0818
immature alpha-beta T cell7.92e-0818
motile cell1.96e-07386
T cell2.41e-0725
pro-T cell2.41e-0725
stuff accumulating cell4.23e-0787
stem cell9.54e-07441
Uber Anatomy
Ontology termp-valuen
hemolymphoid system3.12e-30108
hematopoietic system1.24e-2998
blood island1.24e-2998
immune system2.33e-2393
bone marrow1.98e-2276
bone element2.46e-1982
skeletal element1.29e-1590
skeletal system2.27e-13100
connective tissue1.39e-12371
lateral plate mesoderm2.12e-08203
blood4.84e-0815
haemolymphatic fluid4.84e-0815
organism substance4.84e-0815


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#1066445.360256373075030.001211145381643620.00816438472300254



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.

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