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Coexpression cluster:C3690: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3690_CD4_CD14CD16_optic_substantia_acute_Eosinophils_migratory
|full_id=C3690_CD4_CD14CD16_optic_substantia_acute_Eosinophils_migratory
|id=C3690
|id=C3690

Revision as of 16:39, 12 September 2012


Full id: C3690_CD4_CD14CD16_optic_substantia_acute_Eosinophils_migratory



Phase1 CAGE Peaks

Hg19::chr17:76124760..76124775,-p2@TMC6
Hg19::chr17:76124788..76124804,-p3@TMC6
Hg19::chr17:76124812..76124851,-p1@TMC6


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
hematopoietic stem cell1.57e-50172
angioblastic mesenchymal cell1.57e-50172
hematopoietic oligopotent progenitor cell1.97e-49165
hematopoietic multipotent progenitor cell1.97e-49165
hematopoietic cell1.25e-48182
leukocyte1.39e-40140
nongranular leukocyte7.23e-35119
hematopoietic lineage restricted progenitor cell2.09e-34124
myeloid cell8.50e-32112
common myeloid progenitor8.50e-32112
myeloid leukocyte9.77e-2376
myeloid lineage restricted progenitor cell3.22e-1970
granulocyte monocyte progenitor cell2.61e-1871
monopoietic cell1.20e-1763
monocyte1.20e-1763
monoblast1.20e-1763
promonocyte1.20e-1763
macrophage dendritic cell progenitor3.85e-1765
CD14-positive, CD16-negative classical monocyte5.24e-1642
lymphocyte2.57e-1553
common lymphoid progenitor2.57e-1553
lymphoid lineage restricted progenitor cell3.27e-1552
classical monocyte5.04e-1545
mature alpha-beta T cell1.05e-1118
alpha-beta T cell1.05e-1118
immature T cell1.05e-1118
mature T cell1.05e-1118
immature alpha-beta T cell1.05e-1118
T cell2.88e-1025
pro-T cell2.88e-1025
CD8-positive, alpha-beta T cell5.83e-0811
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.96e-20102
blood island2.96e-20102
hemolymphoid system1.24e-18112
bone marrow3.33e-1380
immune system5.25e-11115
bone element9.26e-1186
adult organism5.76e-08115
Disease
Ontology termp-valuen
leukemia1.76e-0839
myeloid leukemia1.81e-0831
hematologic cancer5.61e-0751
immune system cancer5.61e-0751


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
ATF3#467322.46317452600878.81932387510763e-050.00129547308887815
E2F1#186934.907389214879320.008460985347239390.0325029186258261
E2F6#187635.017155731697390.00791769806886330.0321857569910483
EBF1#187938.9064668465690.00141523283560980.00914638008157502
EGR1#195834.988179094810140.008056488137383440.0320379074964851
ELF1#199734.258097958807540.01295179875054610.0461852263626155
GATA1#2623313.56030814380040.0004009615963782630.00387705102899263
HMGN3#932438.178547723350590.001827766942164210.0108620775960333
MAX#414936.452555509007120.003721913834265510.0186370503397831
SIN3A#2594235.408884726815140.006318961977991520.0276440359409985
TAF7#6879311.43306940492390.0006690181981945830.00542397078103121
TFAP2A#7020316.5186343730450.0002218033880766340.0024807157900338
TFAP2C#7022310.80922860986020.0007916746575753130.00615420242370734
USF1#739136.361499277207960.00388404057290560.019013138663871
USF2#7392312.99219738506960.0004558979393427810.00421358627318768
ZEB1#6935316.88843201754390.0002075486917327580.00242625675127351



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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