Coexpression cluster:C2905: Difference between revisions

Revision as of 15:48, 26 November 2012

Full id: C2905_granulocyte_lymphoma_acute_Hodgkin_CD34_CD133_neuroblastoma

Phase1 CAGE Peaks

Hg19::chr7:92463153..92463169,-	p8@CDK6
Hg19::chr7:92463172..92463183,-	p12@CDK6
Hg19::chr7:92463210..92463231,-	p3@CDK6
Hg19::chr7:92463234..92463293,-	p2@CDK6

Enriched pathways on this co-expression clusterSummary: 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. Analyst: Emmanuel Dimont link to source dataset data

No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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. Analyst: Erik Arner link to source dataset data

No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji links to source dataset disease_data

Disease
Ontology term	p-value	n
hematologic cancer	6.09e-14	51
immune system cancer	6.09e-14	51
cancer	4.27e-11	235
disease of cellular proliferation	1.75e-10	239
leukemia	3.56e-10	39
myeloid leukemia	3.28e-08	31
organ system cancer	4.64e-08	137

Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon link to source data Novel motifs data Jaspar motifs data

Novel motifs

JASPAR motifs

Motifs	-log10(p-value)
{{{tfbs_overrepresentation_jaspar}}}

ENCODE TF ChIP-seq peak enrichment analysisSummary: 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. Analyst: Erik Arner link to source dataset data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
CCNT2#905	4	6.33620157696263	0.000620310058721564	0.00513714711147581
CHD2#1106	4	10.3440228341169	8.73193255208051e-05	0.0012937357125929
CTCF#10664	4	5.36025637307503	0.00121114538164362	0.00820037682421253
E2F6#1876	4	5.01715573169739	0.0015780219347306	0.00999436220990473
EBF1#1879	4	8.906466846569	0.0001588790747201	0.00200134744719485
EGR1#1958	4	4.98817909481014	0.00161501150007605	0.0101669792680195
ELF1#1997	4	4.25809795880754	0.00304152556578124	0.0161286564389249
EP300#2033	4	6.7739417262232	0.000474845982144264	0.00435479799167236
GABPB1#2553	4	7.06768383618217	0.000400687686442317	0.00390914724748707
HDAC2#3066	4	13.4156202366263	3.0859005065161e-05	0.000628732662895113
HEY1#23462	4	4.04011104310571	0.0037530463691798	0.0186640831270306
MXI1#4601	4	9.9615716287593	0.000101522475495045	0.00142780848616038
PBX3#5090	4	21.9145126867441	4.33289161192893e-06	0.000136796513620993
RAD21#5885	4	10.3550338954563	8.6948481184721e-05	0.00130023087434866
SIN3A#25942	4	5.40888472681514	0.00116817238488516	0.0079818616751731
SMC3#9126	4	15.0449328449328	1.95092670935632e-05	0.000439691054377352
TAF1#6872	4	3.34304628574529	0.00800566489870165	0.0323356783987122
ZBTB7A#51341	4	7.3519093078759	0.00034222354001599	0.00347308175062967
ZNF143#7702	4	13.5008765522279	3.00867915035614e-05	0.000622101448790427
ZNF263#10127	4	8.22184163701068	0.000218787118095832	0.00250026346720764

Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. Analyst:NA link to data source data

This analysis result is provided for C0 - C305 clusters.

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 |tf_chipseq_enrich=CCNT2#905;4:6.33620157696263:0.000620310058721564:0.00513714711147581!CHD2#1106;4:10.3440228341169:8.73193255208051e-05:0.0012937357125929!CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00820037682421253!E2F6#1876;4:5.01715573169739:0.0015780219347306:0.00999436220990473!EBF1#1879;4:8.906466846569:0.0001588790747201:0.00200134744719485!EGR1#1958;4:4.98817909481014:0.00161501150007605:0.0101669792680195!ELF1#1997;4:4.25809795880754:0.00304152556578124:0.0161286564389249!EP300#2033;4:6.7739417262232:0.000474845982144264:0.00435479799167236!GABPB1#2553;4:7.06768383618217:0.000400687686442317:0.00390914724748707!HDAC2#3066;4:13.4156202366263:3.0859005065161e-05:0.000628732662895113!HEY1#23462;4:4.04011104310571:0.0037530463691798:0.0186640831270306!MXI1#4601;4:9.9615716287593:0.000101522475495045:0.00142780848616038!PBX3#5090;4:21.9145126867441:4.33289161192893e-06:0.000136796513620993!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00130023087434866!SIN3A#25942;4:5.40888472681514:0.00116817238488516:0.0079818616751731!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.000439691054377352!TAF1#6872;4:3.34304628574529:0.00800566489870165:0.0323356783987122!ZBTB7A#51341;4:7.3519093078759:0.00034222354001599:0.00347308175062967!ZNF143#7702;4:13.5008765522279:3.00867915035614e-05:0.000622101448790427!ZNF263#10127;4:8.22184163701068:0.000218787118095832:0.00250026346720764
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+|tfbs_overrepresentation_for_novel_motifs=1.44014,1.54039,1.42265,0.741427,0.534346,0.739643,0.821651,0.395818,2.69906,1.44778,0.706765,0.867962,0.341754,0.809319,0.532789,1.37557,2.39977,0.471262,0.356737,0.635753,0.581762,0.169357,0.731221,0.528529,0.632849,0.892087,5.22228,1.72987,0.537869,0.297585,2.75338,1.09415,0.433165,0.344471,0.49475,1.00622,0.491074,1.75478,0.463978,1.72725,0.493145,1.59701,0.183156,0.53106,1.08066,1.49501,0.822818,0.694903,0.173425,0.538016,0.90714,0.83543,0.25073,1.17354,1.33024,0.812467,0.54284,0.777235,0.297448,0.776148,1.13655,0.825354,0.393426,1.02706,0.844545,0.991076,1.42026,1.79268,1.08337,1.62905,0.650393,0.402607,3.64335,1.32819,0.336329,1.54953,0.305238,1.00941,1.08,1.51572,0.362435,1.02594,0.844168,0.399165,2.84439,0.109222,1.84544,0.291738,0.934646,1.89266,1.51507,1.24792,1.11156,0.441618,0.535192,0.456994,0.934671,1.15558,0.939507,0.272395,0.465545,1.1057,1.14983,1.05974,0.979006,0.701817,1.04326,0.805616,0.632569,0.516141,0.594299,1.14697,0.575476,0.717043,1.46636,0.489254,1.85914,1.63159,0.988625,0.444962,1.31973,0.932085,0.736652,0.856196,1.57854,1.0102,0.814847,1.11673,1.36323,0.458105,1.24863,0.68598,1.37788,0.852645,1.52813,0.283547,0.676268,0.729481,1.48509,2.34913,4.19009,1.44718,0.8167,1.15194,0.980848,0.768101,0.963351,2.1895,0.661255,0.437774,2.68745,0.521611,1.24902,0.383416,0.824835,1.65997,0.917558,0.518428,0.632914,0.600782,1.44595,1.23002,1.07918,0.604379,0.997702,0.843324,0.423521,0.820225,0.156682
 }}

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Coexpression cluster:C2905: Difference between revisions

From FANTOM5_SSTAR

Revision as of 15:48, 26 November 2012

Phase1 CAGE Peaks

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	Mozilla Cavendish skin modified by DaSch for the Web Community Wiki GitHub project page – Report a bug – Skin version: 2.6.0