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Coexpression cluster:C1964: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1964_Mast_Hepatocyte_CD14_granulocyte_liver_Macrophage_acute
|full_id=C1964_Mast_Hepatocyte_CD14_granulocyte_liver_Macrophage_acute
|id=C1964
|id=C1964

Revision as of 14:36, 12 September 2012


Full id: C1964_Mast_Hepatocyte_CD14_granulocyte_liver_Macrophage_acute



Phase1 CAGE Peaks

Hg19::chr5:75699040..75699090,+p3@IQGAP2
Hg19::chr5:75699091..75699117,+p1@IQGAP2
Hg19::chr5:75699125..75699136,+p7@IQGAP2
Hg19::chr5:75699154..75699180,+p2@IQGAP2
Hg19::chr5:75699195..75699206,+p6@IQGAP2


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 cell3.31e-54172
angioblastic mesenchymal cell3.31e-54172
hematopoietic oligopotent progenitor cell2.47e-51165
hematopoietic multipotent progenitor cell2.47e-51165
hematopoietic cell6.20e-50182
leukocyte6.18e-43140
hematopoietic lineage restricted progenitor cell6.76e-38124
myeloid cell9.92e-36112
common myeloid progenitor9.92e-36112
nongranular leukocyte1.70e-35119
myeloid leukocyte1.66e-2676
granulocyte monocyte progenitor cell2.36e-2471
myeloid lineage restricted progenitor cell3.21e-2470
CD14-positive, CD16-negative classical monocyte1.75e-2042
macrophage dendritic cell progenitor1.81e-2065
monopoietic cell2.19e-2063
monocyte2.19e-2063
monoblast2.19e-2063
promonocyte2.19e-2063
classical monocyte8.18e-1845
lymphocyte2.01e-1353
common lymphoid progenitor2.01e-1353
lymphoid lineage restricted progenitor cell3.89e-1352
T cell2.69e-1025
pro-T cell2.69e-1025
mature alpha-beta T cell5.09e-1018
alpha-beta T cell5.09e-1018
immature T cell5.09e-1018
mature T cell5.09e-1018
immature alpha-beta T cell5.09e-1018
CD8-positive, alpha-beta T cell6.99e-0711
Uber Anatomy
Ontology termp-valuen
hematopoietic system2.10e-27102
blood island2.10e-27102
hemolymphoid system7.71e-24112
immune system1.36e-20115
bone marrow7.95e-2080
bone element3.30e-1886
skeletal element1.39e-11101
skeletal system1.39e-11101
adult organism1.93e-11115
Disease
Ontology termp-valuen
leukemia1.87e-0939
myeloid leukemia5.40e-0831
hematologic cancer9.90e-0851
immune system cancer9.90e-0851


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
CCNT2#90556.336201576962639.78880505817628e-050.00139168664779591
CTCF#1066455.360256373075030.0002259278299937090.00250219264440222
CTCFL#140690519.74647435897443.32745051287657e-071.65957786109989e-05
E2F6#187655.017155731697390.0003144978599297790.00323190416148836
EBF1#187958.9064668465691.78355672307702e-050.000406709346291356
EGR1#195854.988179094810140.0003237398000590710.00331091470606829
ELF1#199754.258097958807540.0007142416939776840.00573761158967275
EP300#203356.77394172622327.00901578206049e-050.00110995390335499
ETS1#211359.728760922202341.14685159850452e-050.000292350583588512
GABPB1#255357.067683836182175.6685482528729e-050.000949506833972402
GATA1#2623513.56030814380042.17950082879909e-067.83832255712631e-05
GATA2#2624512.7449317335542.9719152914525e-060.000101300215771543
HDAC2#3066513.41562023662632.29961139448262e-068.18572305481836e-05
HEY1#2346254.040111043105710.0009288852205177990.00674864998578493
HMGN3#932458.178547723350592.73180911341838e-050.000582854774251894
JUND#372756.994663941871035.97069468343598e-050.000985263678374735
MAX#414956.452555509007128.93743970843928e-050.0013076733898987
MYC#460955.22228187160940.0002573944848850610.00276734842566511
NFKB1#479055.488063424193840.0002008162847462320.00239336436866503
PAX5#507956.669565531177837.57493746384605e-050.0011715073208746
RAD21#5885510.35503389545638.39503550283973e-060.000229942069992415
SMC3#9126515.04493284493281.29633924985553e-065.16946830529445e-05
SP1#666755.69838137814090.000166391843712550.00204516862015947
SPI1#668858.204323508522732.68916109982495e-050.000575519049394709
TAF1#687253.343046285745290.002394600090870310.0135549939777997
TBP#690853.706770687096390.001428755106721120.00920245171698102
TCF12#6938510.63446490218647.34844389925727e-060.000211480885201028
USF1#739156.361499277207969.59569864925045e-050.00137057600003975
USF2#7392512.99219738506962.69963551658264e-069.4359850641357e-05
YY1#752854.911170749853860.00034993140821360.00353140268068607
ZBTB7A#5134157.35190930787594.65425347594289e-050.00081653885229968
ZEB1#6935516.88843201754397.27243686732534e-073.23753637675444e-05
ZNF143#7702513.50087655222792.22790360787208e-067.97942472230973e-05



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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