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Coexpression cluster:C2366: Difference between revisions

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|tf_chipseq_enrich=PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428335629376624!TAL1#6886;2:14.9343083387201:0.00642807757788807:0.0279458016965846
|tf_chipseq_enrich=PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428335629376624!TAL1#6886;2:14.9343083387201:0.00642807757788807:0.0279458016965846
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}}
}}

Revision as of 15:27, 26 November 2012


Full id: C2366_Neutrophils_Eosinophils_leukemia_CD19_caudate_granulocyte_neuroectodermal



Phase1 CAGE Peaks

Hg19::chr16:23847254..23847261,+p2@PRKCB
Hg19::chr16:23847267..23847335,+p1@PRKCB
Hg19::chr16:24060399..24060400,+p@chr16:24060399..24060400
+
Hg19::chr16:24223808..24223818,+p@chr16:24223808..24223818
+


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 cell1.66e-67168
angioblastic mesenchymal cell1.66e-67168
hematopoietic oligopotent progenitor cell4.01e-64161
hematopoietic multipotent progenitor cell4.01e-64161
hematopoietic cell3.23e-63177
leukocyte1.09e-55136
hematopoietic lineage restricted progenitor cell2.36e-47120
nongranular leukocyte4.07e-46115
myeloid cell5.20e-39108
common myeloid progenitor5.20e-39108
myeloid leukocyte2.17e-2872
granulocyte monocyte progenitor cell4.94e-2567
myeloid lineage restricted progenitor cell8.61e-2466
macrophage dendritic cell progenitor2.78e-2261
nucleate cell1.33e-2155
lymphocyte1.37e-2153
common lymphoid progenitor1.37e-2153
lymphoid lineage restricted progenitor cell1.77e-2152
monopoietic cell1.87e-2159
monocyte1.87e-2159
monoblast1.87e-2159
promonocyte1.87e-2159
defensive cell8.57e-2148
phagocyte8.57e-2148
classical monocyte1.79e-1942
CD14-positive, CD16-negative classical monocyte1.79e-1942
lymphocyte of B lineage1.04e-1224
pro-B cell1.04e-1224
mature alpha-beta T cell2.14e-1018
alpha-beta T cell2.14e-1018
immature T cell2.14e-1018
mature T cell2.14e-1018
immature alpha-beta T cell2.14e-1018
B cell2.07e-0814
T cell2.51e-0825
pro-T cell2.51e-0825
stuff accumulating cell1.75e-0787
CD8-positive, alpha-beta T cell4.42e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.54e-3298
blood island1.54e-3298
adult organism3.79e-31114
hemolymphoid system2.54e-28108
bone marrow7.95e-2176
immune system1.84e-2093
bone element6.45e-1882
neural tube1.19e-1656
neural rod1.19e-1656
future spinal cord1.19e-1656
neural keel1.19e-1656
regional part of nervous system7.76e-1653
regional part of brain7.76e-1653
telencephalon6.28e-1534
brain grey matter1.15e-1434
gray matter1.15e-1434
regional part of forebrain1.75e-1441
forebrain1.75e-1441
anterior neural tube1.75e-1441
future forebrain1.75e-1441
cerebral hemisphere1.83e-1432
skeletal element3.79e-1490
regional part of telencephalon5.24e-1432
regional part of cerebral cortex4.23e-1322
neocortex1.19e-1220
central nervous system1.67e-1281
skeletal system1.11e-11100
nervous system4.05e-1189
neurectoderm1.40e-1086
brain1.69e-1068
future brain1.69e-1068
cerebral cortex2.03e-1025
pallium2.03e-1025
blood1.06e-0915
haemolymphatic fluid1.06e-0915
organism substance1.06e-0915
neural plate6.46e-0982
presumptive neural plate6.46e-0982
pre-chordal neural plate3.13e-0761
Disease
Ontology termp-valuen
myeloid leukemia5.22e-1031
hematologic cancer7.36e-1051
immune system cancer7.36e-1051
leukemia5.07e-0939


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
PBX3#5090210.95725634337210.01174530180688030.0428335629376624
TAL1#6886214.93430833872010.006428077577888070.0279458016965846



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.