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Coexpression cluster:C2621: Difference between revisions

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|tf_chipseq_enrich=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360233170911591!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.024052351891028!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365888624709116!MAX#4149;3:4.83941663175534:0.0131573713783684:0.046634857441981!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768390765002418!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444234936852144!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428545128356895!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281048971373971!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162822876646428!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483123225518225
|tf_chipseq_enrich=BATF#10538;2:12.1789008961518:0.00956675880504781:0.0360233170911591!EBF1#1879;3:6.67985013492675:0.00518429411827891:0.024052351891028!IRF4#3662;3:16.4358845150581:0.000366943139555461:0.00365888624709116!MAX#4149;3:4.83941663175534:0.0131573713783684:0.046634857441981!NFKB1#4790;4:5.48806342419384:0.00110219956630198:0.00768390765002418!PAX5#5079;4:6.66956553117783:0.000505277416948326:0.00444234936852144!PBX3#5090;2:10.9572563433721:0.0117453018068803:0.0428545128356895!SPI1#6688;3:6.15324263139204:0.00658038711305903:0.0281048971373971!TCF12#6938;3:7.97584867663982:0.00309092039601307:0.0162822876646428!USF1#7391;3:4.77112445790597:0.0137046588718802:0.0483123225518225
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}}
}}

Revision as of 15:37, 26 November 2012


Full id: C2621_migratory_Eosinophils_Neutrophils_CD14_hairy_immature_Mast



Phase1 CAGE Peaks

Hg19::chr20:4803297..4803323,-p@chr20:4803297..4803323
-
Hg19::chr22:35806477..35806519,+p3@MCM5
Hg19::chr22:35806599..35806615,+p8@MCM5
Hg19::chr6:12061235..12061270,+p@chr6:12061235..12061270
+


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
leukocyte1.70e-82136
nongranular leukocyte6.02e-69115
hematopoietic stem cell1.57e-63168
angioblastic mesenchymal cell1.57e-63168
hematopoietic lineage restricted progenitor cell1.67e-62120
hematopoietic cell8.02e-62177
hematopoietic oligopotent progenitor cell7.11e-59161
hematopoietic multipotent progenitor cell7.11e-59161
myeloid leukocyte1.83e-4672
macrophage dendritic cell progenitor1.73e-4361
defensive cell1.22e-4248
phagocyte1.22e-4248
classical monocyte1.58e-4242
CD14-positive, CD16-negative classical monocyte1.58e-4242
monopoietic cell2.31e-4159
monocyte2.31e-4159
monoblast2.31e-4159
promonocyte2.31e-4159
granulocyte monocyte progenitor cell6.37e-3967
myeloid lineage restricted progenitor cell5.21e-3666
myeloid cell8.40e-33108
common myeloid progenitor8.40e-33108
lymphocyte2.99e-2353
common lymphoid progenitor2.99e-2353
lymphoid lineage restricted progenitor cell1.82e-2252
nucleate cell7.33e-2255
lymphocyte of B lineage2.23e-1924
pro-B cell2.23e-1924
stuff accumulating cell1.52e-1587
dendritic cell9.35e-1210
B cell1.74e-1014
mesenchymal cell1.86e-10354
intermediate monocyte2.45e-109
CD14-positive, CD16-positive monocyte2.45e-109
granulocyte2.84e-108
conventional dendritic cell5.92e-108
connective tissue cell1.14e-09361
blood cell3.66e-0811
Langerhans cell3.33e-075
motile cell5.06e-07386
Uber Anatomy
Ontology termp-valuen
hematopoietic system5.61e-4798
blood island5.61e-4798
hemolymphoid system6.33e-43108
bone marrow1.23e-3476
immune system1.73e-3493
bone element1.61e-3082
skeletal element6.29e-2690
skeletal system4.38e-22100
adult organism2.28e-16114
neural tube3.14e-1356
neural rod3.14e-1356
future spinal cord3.14e-1356
neural keel3.14e-1356
regional part of nervous system1.34e-1253
regional part of brain1.34e-1253
lateral plate mesoderm1.48e-11203
brain grey matter7.72e-1134
gray matter7.72e-1134
telencephalon1.03e-1034
regional part of forebrain2.73e-1041
forebrain2.73e-1041
anterior neural tube2.73e-1041
future forebrain2.73e-1041
regional part of telencephalon1.03e-0932
cerebral hemisphere1.23e-0932
blood4.73e-0915
haemolymphatic fluid4.73e-0915
organism substance4.73e-0915
regional part of cerebral cortex5.94e-0922
connective tissue6.34e-09371
brain4.01e-0868
future brain4.01e-0868
neocortex7.23e-0820
central nervous system1.86e-0781
cerebral cortex2.39e-0725
pallium2.39e-0725
neural plate7.08e-0782
presumptive neural plate7.08e-0782


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
BATF#10538212.17890089615180.009566758805047810.0360233170911591
EBF1#187936.679850134926750.005184294118278910.024052351891028
IRF4#3662316.43588451505810.0003669431395554610.00365888624709116
MAX#414934.839416631755340.01315737137836840.046634857441981
NFKB1#479045.488063424193840.001102199566301980.00768390765002418
PAX5#507946.669565531177830.0005052774169483260.00444234936852144
PBX3#5090210.95725634337210.01174530180688030.0428545128356895
SPI1#668836.153242631392040.006580387113059030.0281048971373971
TCF12#693837.975848676639820.003090920396013070.0162822876646428
USF1#739134.771124457905970.01370465887188020.0483123225518225



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.