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Coexpression cluster:C3460: Difference between revisions

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|tf_chipseq_enrich=NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324647289747983!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381147948745364!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287470765762101!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00560735316245685
|tf_chipseq_enrich=NFYA#4800;2:12.2837204665537:0.00851601140372443:0.0324647289747983!NFYB#4801;2:11.1731955023576:0.0102546713505453:0.0381147948745364!STAT1#6772;2:13.8043916647995:0.00677093170844408:0.0287470765762101!STAT2#6773;2:43.5091807909604:0.000696899089886823:0.00560735316245685
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}}
}}

Revision as of 16:09, 26 November 2012


Full id: C3460_Mast_CD14_malignant_Neutrophils_epidermoid_Smooth_squamous



Phase1 CAGE Peaks

Hg19::chr14:91581610..91581632,-p@chr14:91581610..91581632
-
Hg19::chr7:92747245..92747252,-p3@SAMD9
Hg19::chr7:92747269..92747332,-p1@SAMD9


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
leukocyte2.32e-44136
hematopoietic stem cell9.42e-44168
angioblastic mesenchymal cell9.42e-44168
hematopoietic oligopotent progenitor cell1.53e-42161
hematopoietic multipotent progenitor cell1.53e-42161
hematopoietic cell2.65e-42177
nongranular leukocyte2.22e-41115
hematopoietic lineage restricted progenitor cell6.17e-41120
myeloid leukocyte1.91e-3172
myeloid lineage restricted progenitor cell7.20e-2666
myeloid cell1.04e-25108
common myeloid progenitor1.04e-25108
granulocyte monocyte progenitor cell3.78e-2567
monopoietic cell7.75e-2559
monocyte7.75e-2559
monoblast7.75e-2559
promonocyte7.75e-2559
classical monocyte9.64e-2542
CD14-positive, CD16-negative classical monocyte9.64e-2542
macrophage dendritic cell progenitor2.38e-2361
defensive cell8.91e-2348
phagocyte8.91e-2348
lymphoid lineage restricted progenitor cell9.78e-1652
mesenchymal cell1.05e-15354
lymphocyte3.77e-1553
common lymphoid progenitor3.77e-1553
connective tissue cell1.76e-14361
nucleate cell4.74e-1455
motile cell1.10e-11386
multi fate stem cell4.43e-09427
somatic stem cell6.53e-09433
stem cell1.13e-08441
lymphocyte of B lineage3.51e-0824
pro-B cell3.51e-0824
stuff accumulating cell9.55e-0887
T cell3.15e-0725
pro-T cell3.15e-0725
mature alpha-beta T cell5.07e-0718
alpha-beta T cell5.07e-0718
immature T cell5.07e-0718
mature T cell5.07e-0718
immature alpha-beta T cell5.07e-0718
Uber Anatomy
Ontology termp-valuen
hematopoietic system4.57e-3498
blood island4.57e-3498
hemolymphoid system1.18e-31108
bone marrow8.83e-2376
immune system1.62e-2293
bone element1.79e-1982
skeletal element2.39e-1790
skeletal system9.19e-15100
connective tissue7.52e-13371
blood3.49e-1115
haemolymphatic fluid3.49e-1115
organism substance3.49e-1115
lateral plate mesoderm1.83e-08203


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
NFYA#4800212.28372046655370.008516011403724430.0324647289747983
NFYB#4801211.17319550235760.01025467135054530.0381147948745364
STAT1#6772213.80439166479950.006770931708444080.0287470765762101
STAT2#6773243.50918079096040.0006968990898868230.00560735316245685



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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