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Coexpression cluster:C3612: Difference between revisions

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|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461615844694497
|tf_chipseq_enrich=ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461615844694497
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}}
}}

Revision as of 16:14, 26 November 2012


Full id: C3612_Mast_granulocyte_CD14_migratory_Neutrophils_Whole_acute



Phase1 CAGE Peaks

Hg19::chr17:19976904..19976915,+p8@SPECC1
Hg19::chr17:19976931..19976957,+p3@SPECC1
Hg19::chr17:19976961..19976972,+p6@SPECC1


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>disease_data<br>


Cell Type
Ontology termp-valuen
myeloid cell2.73e-46108
common myeloid progenitor2.73e-46108
myeloid leukocyte7.78e-4172
hematopoietic stem cell6.81e-36168
angioblastic mesenchymal cell6.81e-36168
myeloid lineage restricted progenitor cell1.14e-3566
granulocyte monocyte progenitor cell1.73e-3567
hematopoietic oligopotent progenitor cell6.66e-33161
hematopoietic multipotent progenitor cell6.66e-33161
hematopoietic cell6.68e-32177
monopoietic cell1.20e-3159
monocyte1.20e-3159
monoblast1.20e-3159
promonocyte1.20e-3159
macrophage dendritic cell progenitor7.22e-3061
leukocyte2.67e-28136
defensive cell4.62e-2748
phagocyte4.62e-2748
classical monocyte3.31e-2542
CD14-positive, CD16-negative classical monocyte3.31e-2542
hematopoietic lineage restricted progenitor cell1.06e-20120
nongranular leukocyte2.20e-19115
stuff accumulating cell1.74e-1387
mesenchymal cell3.07e-07354
connective tissue cell5.92e-07361
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.00e-4098
blood island2.00e-4098
bone marrow4.17e-3576
hemolymphoid system1.44e-34108
adult organism1.40e-33114
bone element9.75e-3382
skeletal element4.81e-2990
immune system8.09e-2993
skeletal system2.59e-25100
neural tube2.94e-1556
neural rod2.94e-1556
future spinal cord2.94e-1556
neural keel2.94e-1556
telencephalon5.81e-1534
regional part of forebrain8.21e-1541
forebrain8.21e-1541
anterior neural tube8.21e-1541
future forebrain8.21e-1541
regional part of nervous system1.09e-1453
regional part of brain1.09e-1453
brain grey matter1.26e-1434
gray matter1.26e-1434
brain1.50e-1468
future brain1.50e-1468
cerebral hemisphere6.35e-1432
regional part of telencephalon7.89e-1432
central nervous system8.62e-1381
musculoskeletal system1.78e-12167
neural plate1.34e-1182
presumptive neural plate1.34e-1182
neurectoderm6.92e-1186
regional part of cerebral cortex7.84e-1122
nervous system1.04e-1089
cerebral cortex1.43e-1025
pallium1.43e-1025
tissue2.03e-10773
pre-chordal neural plate2.74e-1061
lateral plate mesoderm5.09e-10203
neocortex1.10e-0920
ecto-epithelium5.04e-07104
Disease
Ontology termp-valuen
myeloid leukemia5.95e-0831
leukemia1.06e-0739


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
ELF1#199734.258097958807540.01295179875054610.0461615844694497



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.