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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3602_Mast_chronic_leukemia_hairy_acute_biphenotypic_CD14CD16
|full_id=C3602_Mast_chronic_leukemia_hairy_acute_biphenotypic_CD14CD16
|id=C3602
|id=C3602

Revision as of 16:33, 12 September 2012


Full id: C3602_Mast_chronic_leukemia_hairy_acute_biphenotypic_CD14CD16



Phase1 CAGE Peaks

Hg19::chr16:89043500..89043528,-p3@CBFA2T3
Hg19::chr16:89043559..89043601,-p4@CBFA2T3
Hg19::chr16:89043605..89043625,-p6@CBFA2T3


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 cell2.78e-69172
angioblastic mesenchymal cell2.78e-69172
hematopoietic oligopotent progenitor cell2.54e-65165
hematopoietic multipotent progenitor cell2.54e-65165
hematopoietic cell1.05e-62182
myeloid cell3.30e-58112
common myeloid progenitor3.30e-58112
leukocyte2.06e-40140
hematopoietic lineage restricted progenitor cell3.53e-37124
nongranular leukocyte3.98e-34119
myeloid lineage restricted progenitor cell1.93e-3170
myeloid leukocyte9.07e-3176
granulocyte monocyte progenitor cell2.30e-3071
monopoietic cell2.23e-2563
monocyte2.23e-2563
monoblast2.23e-2563
promonocyte2.23e-2563
macrophage dendritic cell progenitor5.79e-2565
CD14-positive, CD16-negative classical monocyte8.89e-2242
classical monocyte2.22e-1945
lymphocyte of B lineage1.07e-1324
pro-B cell1.07e-1324
mesenchymal cell1.19e-11358
connective tissue cell9.81e-11365
B cell6.87e-1014
intermediate monocyte3.16e-099
CD14-positive, CD16-positive monocyte3.16e-099
lymphocyte2.40e-0853
common lymphoid progenitor2.40e-0853
motile cell3.44e-08390
lymphoid lineage restricted progenitor cell5.06e-0852
histamine secreting cell8.89e-075
biogenic amine secreting cell8.89e-075
granulocytopoietic cell8.89e-075
mast cell8.89e-075
mast cell progenitor8.89e-075
basophil mast progenitor cell8.89e-075
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.54e-33102
blood island1.54e-33102
hemolymphoid system2.31e-32112
bone marrow1.36e-2580
adult organism4.17e-24115
bone element2.64e-2286
immune system3.72e-21115
skeletal element1.30e-16101
skeletal system1.30e-16101
connective tissue3.61e-10375
lateral plate mesoderm5.79e-08216
blood1.24e-0715
haemolymphatic fluid1.24e-0715
organism substance1.24e-0715
Disease
Ontology termp-valuen
myeloid leukemia2.38e-3031
leukemia4.09e-2939
hematologic cancer3.43e-2251
immune system cancer3.43e-2251
chronic leukemia2.39e-078


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#90536.336201576962630.003930750035764890.0189784847203203
E2F6#187635.017155731697390.00791769806886330.0321582199818781
EBF1#187938.9064668465690.00141523283560980.0091435510125736
EGR1#195834.988179094810140.008056488137383440.0320110924321929
ELF1#199734.258097958807540.01295179875054610.0461537092161964
ETS1#211339.728760922202340.001085840092584840.00761305407018446
GABPB1#255337.067683836182170.002832212825417420.0153914806573926
GATA1#2623313.56030814380040.0004009615963782630.00387525709459091
GATA2#2624312.7449317335540.0004829527704283790.0043674001550584
HDAC2#3066313.41562023662630.0004140761399857210.0039079792141667
HMGN3#932438.178547723350590.001827766942164210.0108608415835622
MAX#414936.452555509007120.003721913834265510.0186299045740165
MXI1#460139.96157162875930.001011470541259020.00719548885352163
MYC#460935.22228187160940.007020843755740150.0294099912163383
NFKB1#479035.488063424193840.006049381815655430.0269294312878922
PAX5#507936.669565531177830.003370290999677260.017272183213862
PBX3#5090321.91451268674419.49854535978121e-050.00136472496743732
REST#597839.650028716128020.001112636247114590.00766760917270872
SIN3A#2594235.408884726815140.006318961977991520.0276232083219395
SPI1#668838.204323508522730.001810593189410520.0108995643615681
TAL1#6886329.86861667744023.75103522793067e-050.00071947542363609
TCF12#6938310.63446490218640.0008313523990202070.00628761048600705
USF1#739136.361499277207960.00388404057290560.0190024506204004
YY1#752834.911170749853860.008441455341808260.0328851189691191
ZBTB7A#5134137.35190930787590.002516255860282270.0139970836640223



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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