Personal tools

Coexpression cluster:C1835

From FANTOM5_SSTAR

Revision as of 14:27, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1835_CD14_Mast_Natural_Eosinophils_Peripheral_immature_Basophils



Phase1 CAGE Peaks

Hg19::chr1:150583933..150583944,-p@chr1:150583933..150583944
-
Hg19::chr1:150584006..150584024,-p1@AK129725
Hg19::chr1:150584301..150584312,+p@chr1:150584301..150584312
+
Hg19::chr1:150584909..150584912,+p@chr1:150584909..150584912
+
Hg19::chr1:204381399..204381426,+p@chr1:204381399..204381426
+


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
leukocyte4.07e-33140
CD14-positive, CD16-negative classical monocyte4.83e-3142
hematopoietic stem cell1.02e-27172
angioblastic mesenchymal cell1.02e-27172
classical monocyte2.23e-2745
hematopoietic oligopotent progenitor cell7.28e-25165
hematopoietic multipotent progenitor cell7.28e-25165
myeloid leukocyte3.33e-2476
hematopoietic cell3.76e-24182
nongranular leukocyte5.41e-24119
hematopoietic lineage restricted progenitor cell7.36e-24124
granulocyte monocyte progenitor cell1.68e-2071
macrophage dendritic cell progenitor2.82e-1965
myeloid cell4.35e-19112
common myeloid progenitor4.35e-19112
monopoietic cell5.07e-1863
monocyte5.07e-1863
monoblast5.07e-1863
promonocyte5.07e-1863
myeloid lineage restricted progenitor cell1.31e-1770
mesenchymal cell1.83e-11358
connective tissue cell2.27e-11365
intermediate monocyte1.02e-079
CD14-positive, CD16-positive monocyte1.02e-079
multi fate stem cell1.05e-07430
stem cell1.27e-07444
motile cell1.28e-07390
granulocyte1.32e-078
somatic stem cell2.69e-07436
Uber Anatomy
Ontology termp-valuen
hematopoietic system1.49e-24102
blood island1.49e-24102
hemolymphoid system1.87e-21112
bone marrow1.25e-1880
bone element3.81e-1786
immune system5.15e-15115
skeletal element7.67e-14101
skeletal system7.67e-14101
connective tissue1.03e-10375
lateral plate mesoderm5.79e-08216


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#10538314.61468107538220.0006498237314125670.00532331482351534
BCL11A#53335317.02167306216420.000414967457127050.00390474693710172
CEBPB#105146.376918100659850.001113944176677320.00765439935969486
EP300#203345.419153380978560.00209386927943890.0121180102890014
FOS#235335.398773185336640.01153895317278740.0421930092575011
FOSL2#2355413.54416048364945.7953819349229e-050.000964717714219657
FOXA1#316948.865135799508360.0003075468591372710.00316732929902746
FOXA2#3170314.77827825159910.0006289192851194480.00517438957134
GABPB1#255345.654147068945740.001776696502096670.0109099486113872
GATA2#262437.64695904013240.004279061879252130.0203303131474485
GTF2F1#2962410.19172870140610.000177833889427640.00215887406462087
HNF4A#3172313.87937421777220.0007561408847434270.0059456857296882
HNF4G#3174317.25205351586810.0003988503772822420.00389558912868045
IRF4#3662313.14870761204650.0008860469322808430.00660465745203619
JUN#3725410.01026335386910.0001908531347801070.00230566923577785
JUND#372745.595731153496820.001849593301755460.0109345451625743
MAFF#23764333.78921389396715.44627740085589e-050.000923232860684935
MEF2A#4205311.24593854578640.001399366787411950.0091035547471357
MXI1#460147.969257303007440.0004668546380070170.00429508734485684
NFKB1#479044.390450739355070.004707732692524960.0222043487637002
NR3C1#290838.983813998703820.002687995788940450.0147963733832895
POU2F2#545235.463674434645510.01115650094469780.0410185806577233
REST#597847.720022972902420.0005286363773650570.00457341406690103
RFX5#599349.638328661756080.000221480125815720.00249688718264982
SIN3A#2594244.327107781452110.004977052855762880.0232457592774482
SMARCC1#6599326.19801559177890.0001159625626060410.00157674965186985
SMARCC2#6601356.49322465613861.17726327391127e-050.000298355251307982
SP1#666744.558705102512720.00407573565781680.019486621331566
SPI1#668846.563458806818180.0009957429636454020.00714247248490125
SRF#672238.278306957300690.003404846073776150.0173632187060111
STAT3#677448.415571997723390.0003771527211598630.00374282146001662



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C1835&oldid=2136444"