Personal tools

Coexpression cluster:C1831: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 1: Line 1:
{{Coexpression_clusters
{{Coexpression_clusters
|coexpression_dpi_cluster_scores_median=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0319790978673642,0.0342676336102362,0,0.410516934126256,0.148312581064756,0.250876864750288,0,0,0,0.032404058578668,0,0.111800154394222,0.224782856999752,0.503859919236496,0.401241286650242,0,0,0,0.173310323757815,0.230032810011795,0.0943257785523457,0.285493430983262,0.161542543663586,0.117173940088031,0.520489138557432,0.25900201931402,0.239850714044648,0.475866924840341,0.526989891210352,0.371855321441455,0.229182412925464,0.104796384789156,0.223799672996739,0.475495750266528,0.466211111825445,0.452040556201374,0.365376626635383,0.201361420919153,0.267746377672919,0.579680108112998,0.583983437331127,0.358563961992262,0.414296634748979,0.309908167440964,0.371427476070495,0.534228984731047,0.634859870494673,0.585253288788725,0,0.0837191039350518,0.211914668893199,0.193581802139666,0.114061526358155,0.0718141417798722,0,0.0787890013723437,0,0,0,0,0.0552560033931503,0,0,0,0,0,0,0,0,0,0,0.0779888366877325,0.1528008311411,0,0,0,0.168334756349589,0,0,0.112137584435249,0,0.187973878616286,0.0523442574910016,0,0,0,0,0,0,0.310768747319633,0,0.140891414760007,0.128278866336583,0,0,0,0,0.0609149782727745,0.0523039447392876,0,0,0,0.0797623568580576,0.102927476286267,0.0587388785772559,0,0,0,0,0,0,0,0,0.0392295810357272,0,0.0316784990343826,0.80440461056267,0,0,0,0,0,0,0,0.13718235424895,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.595818640136886,0.688224224545008,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0148879263042408,0,0,0,0.0677314085379025,0,0,0.0068157636808565,0,0.131942369721337,0,0,0,0,0,0,0,0.0477396614475454,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0446915468534936,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.00736524432192352,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.081825314342242,0.270613563765641,0.212510452163498,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0781053106522872,0.0848005428997621,0.141458900963942,0,0,0,0,0.115211800265726,0.412399249379803,0.50206274394636,0.61222819965816,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.150306889650249,0.270179472213526,0.115854728469987,0,0,0,0,0.0620032815069762,0,0,0,0,0,0,0,0,0,0,0,0,0.00684750411755274,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0425916600387234,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0521599633818348,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0642154945051553,0,0,0,0,0,0,0,0,0,0.0670147110949639,0,0,0,0,0,0,0.0389897101274218,0.0125181617248143,0,0,0,0,0.103383213163165,0,0,0,0,0.123723537352191,0,0,0,0,0,0.0504125515893149,0,0,0,0,0.0408567533019575,0,0,0,0,0,0,0,0,0,0.0794615586823006,0,0,0,0,0,0,0,0,0,0,0,0,0.0321956448428329,0,0,0.00446916133298671,0,0,0,0,0,0,0,0,0.0777538866750895,0,0,0,0,0,0.0544421905770192,0,0,0,0,0,0.0505977919678937,0,0,0,0,0,0,0,0,0,0,0.0201478867126564,0.161658510430072,0.0428463959634473,0,0,0,0,0,0,0.0695052016201444,0,0.0362531985397609,0,0,0,0,0,0,0,0,0,0,0.020352812583328,0,0.0645768949458293,0,0,0,0,0,0.05690701457802,0,0,0,0,0,0,0,0.0557243212092205,0.258366021761785,0,0.101364614532639,0,0,0,0,0,0,0,0,0,0,0,0.0283286403579212,0,0,0,0,0.0647398703344467,0,0,0.0881268324752877,0,0.0256128589246175,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.084066558699748,0.0196445376878033,0,0,0.078316005475075,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0613201791501264,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0725618668317725,0.0443086593632396,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0450136346124787,0,0,0,0,0,0,0,0,0,0.0270351810347199,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0283831740999027,0,0,0,0,0,0,0,0.052217621604872,0,0,0,0.0890788809625826,0,0,0,0.0279698901802024,0,0.0485170957947049,0,0,0,0,0,0.0849077133655763,0,0,0,0,0,0,0,0,0,0,0.0485707522809905,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0390109377342095,0,0,0,0,0,0,0,0.0562558740333894,0,0,0,0,0,0,0,0,0,0.0980886515842491,0.0421771923324582,0,0,0,1.12719814590291,1.20249649671379,0,0,0,0,0,0.0508240440617333,0,0,0,0,0,0.00451544587654389,0.0300822291072195,0,0,0.0840235651855054,0,0,0,0,0,0,0,0
|full_id=C1831_testis_Eosinophils_CD14_Neutrophils_Basophils_Whole_Natural
|full_id=C1831_testis_Eosinophils_CD14_Neutrophils_Basophils_Whole_Natural
|gostat_on_coexpression_clusters=GO:0048250!mitochondrial iron ion transport!0.0016484163428706!51312$GO:0005381!iron ion transmembrane transporter activity!0.00494524902861179!51312$GO:0046915!transition metal ion transmembrane transporter activity!0.0156599552572707!51312$GO:0006839!mitochondrial transport!0.0156599552572707!51312$GO:0015082!di-, tri-valent inorganic cation transmembrane transporter activity!0.0156599552572707!51312$GO:0006826!iron ion transport!0.0156599552572707!51312$GO:0007005!mitochondrion organization and biogenesis!0.0209584363593548!51312$GO:0000041!transition metal ion transport!0.0210173083716001!51312$GO:0015674!di-, tri-valent inorganic cation transport!0.0451666077946544!51312$GO:0022890!inorganic cation transmembrane transporter activity!0.0451666077946544!51312$GO:0005743!mitochondrial inner membrane!0.045468817457514!51312$GO:0019866!organelle inner membrane!0.045468817457514!51312
|gostat_on_coexpression_clusters=GO:0048250!mitochondrial iron ion transport!0.0016484163428706!51312$GO:0005381!iron ion transmembrane transporter activity!0.00494524902861179!51312$GO:0046915!transition metal ion transmembrane transporter activity!0.0156599552572707!51312$GO:0006839!mitochondrial transport!0.0156599552572707!51312$GO:0015082!di-, tri-valent inorganic cation transmembrane transporter activity!0.0156599552572707!51312$GO:0006826!iron ion transport!0.0156599552572707!51312$GO:0007005!mitochondrion organization and biogenesis!0.0209584363593548!51312$GO:0000041!transition metal ion transport!0.0210173083716001!51312$GO:0015674!di-, tri-valent inorganic cation transport!0.0451666077946544!51312$GO:0022890!inorganic cation transmembrane transporter activity!0.0451666077946544!51312$GO:0005743!mitochondrial inner membrane!0.045468817457514!51312$GO:0019866!organelle inner membrane!0.045468817457514!51312

Revision as of 14:27, 12 September 2012


Full id: C1831_testis_Eosinophils_CD14_Neutrophils_Basophils_Whole_Natural



Phase1 CAGE Peaks

Hg19::chr1:113162293..113162342,-p3@ST7L
Hg19::chr3:39194422..39194451,+p@chr3:39194422..39194451
+
Hg19::chr5:142388947..142388964,+p@chr5:142388947..142388964
+
Hg19::chr6:15248904..15248915,-p2@uc003nbk.2
Hg19::chr8:23386338..23386357,+p8@SLC25A37


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


GO IDGO nameFDR corrected p-value
GO:0048250mitochondrial iron ion transport0.0016484163428706
GO:0005381iron ion transmembrane transporter activity0.00494524902861179
GO:0046915transition metal ion transmembrane transporter activity0.0156599552572707
GO:0006839mitochondrial transport0.0156599552572707
GO:0015082di-, tri-valent inorganic cation transmembrane transporter activity0.0156599552572707
GO:0006826iron ion transport0.0156599552572707
GO:0007005mitochondrion organization and biogenesis0.0209584363593548
GO:0000041transition metal ion transport0.0210173083716001
GO:0015674di-, tri-valent inorganic cation transport0.0451666077946544
GO:0022890inorganic cation transmembrane transporter activity0.0451666077946544
GO:0005743mitochondrial inner membrane0.045468817457514
GO:0019866organelle inner membrane0.045468817457514



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
leukocyte5.45e-37140
hematopoietic stem cell2.42e-36172
angioblastic mesenchymal cell2.42e-36172
hematopoietic cell1.36e-34182
hematopoietic oligopotent progenitor cell5.79e-33165
hematopoietic multipotent progenitor cell5.79e-33165
hematopoietic lineage restricted progenitor cell2.82e-30124
nongranular leukocyte1.88e-28119
CD14-positive, CD16-negative classical monocyte4.13e-2442
classical monocyte7.01e-2345
myeloid leukocyte2.22e-2076
myeloid cell1.86e-19112
common myeloid progenitor1.86e-19112
granulocyte monocyte progenitor cell2.79e-1771
myeloid lineage restricted progenitor cell8.58e-1770
macrophage dendritic cell progenitor2.72e-1565
monopoietic cell2.00e-1463
monocyte2.00e-1463
monoblast2.00e-1463
promonocyte2.00e-1463
lymphocyte1.24e-1253
common lymphoid progenitor1.24e-1253
lymphoid lineage restricted progenitor cell2.19e-1252
Uber Anatomy
Ontology termp-valuen
hematopoietic system9.38e-21102
blood island9.38e-21102
hemolymphoid system2.61e-18112
bone marrow4.94e-1480
bone element2.54e-1386
immune system5.18e-09115
skeletal element3.20e-08101
skeletal system3.20e-08101
blood1.58e-0715
haemolymphatic fluid1.58e-0715
organism substance1.58e-0715


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
BRCA1#672312.11053838593430.001127176470125940.00772803672050697
CCNT2#90545.068961261570110.002709998091280770.0148986413989194
CHD2#110636.206413700470110.007774550126275590.0319571095969024
CTCF#1066455.360256373075030.0002259278299937090.00249874792298135
E2F6#187644.013724585357910.006632118233933880.0283003798256924
FOS#235347.198364247115530.0006947858453382510.00559681750106298
JUN#3725410.01026335386910.0001908531347801070.00230540256110335
JUND#372756.994663941871035.97069468343598e-050.0009844859204979
RAD21#588548.284027116365060.0004011622639122450.00386717608277007
REST#597835.790017229676810.009468788694433940.0357033295710155
RFX5#599337.228746496317060.00502918278958660.0234671978090267
SMARCC1#6599217.46534372785260.005008037385199390.0233779294896902
SMC3#912639.02695970695970.002650964449467550.0146403720658845
SPI1#668846.563458806818180.0009957429636454020.00714198196416195
STAT3#677436.311678998292540.007411172122460540.030615275899757
TBP#690853.706770687096390.001428755106721120.00919168132258515
USF1#739145.089199421766370.00266867775360040.0147202934355272
YY1#752843.928936599883080.007193866269917620.0298450861747806
ZEB1#6935310.13305921052630.001895556924357070.0111639355790294



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.