Coexpression cluster:C4522

Full id: C4522_non_parietal_occipital_thymus_temporal_duodenum_Hodgkin

Phase1 CAGE Peaks

Hg19::chr5:81046859..81046902,-	p1@SSBP2
Hg19::chr5:81046904..81046921,-	p2@SSBP2
Hg19::chr5:81046922..81046933,-	p3@SSBP2

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

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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

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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>

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Cell Type

Ontology term	p-value	n
lymphocyte	4.75e-09	53
common lymphoid progenitor	4.75e-09	53
lymphoid lineage restricted progenitor cell	1.19e-08	52
lymphocyte of B lineage	1.61e-08	24
pro-B cell	1.61e-08	24

Uber Anatomy

Ontology term	p-value	n
adult organism	1.67e-30	115
neural tube	5.03e-24	57
neural rod	5.03e-24	57
future spinal cord	5.03e-24	57
neural keel	5.03e-24	57
central nervous system	1.24e-23	82
brain	2.84e-22	69
future brain	2.84e-22	69
regional part of brain	1.01e-21	59
regional part of nervous system	6.59e-20	94
nervous system	6.59e-20	94
anterior neural tube	3.76e-19	42
regional part of forebrain	1.13e-18	41
forebrain	1.13e-18	41
future forebrain	1.13e-18	41
gray matter	1.99e-16	34
brain grey matter	1.99e-16	34
telencephalon	2.39e-16	34
neural plate	6.78e-16	86
presumptive neural plate	6.78e-16	86
regional part of telencephalon	7.47e-16	33
cerebral hemisphere	1.78e-15	32
neurectoderm	2.30e-15	90
anterior region of body	6.10e-14	129
craniocervical region	6.10e-14	129
pre-chordal neural plate	3.50e-13	61
head	2.45e-12	123
cerebral cortex	3.96e-12	25
pallium	3.96e-12	25
regional part of cerebral cortex	5.18e-12	22
neocortex	2.98e-11	20
ectoderm-derived structure	1.92e-10	169
ectoderm	2.64e-10	173
presumptive ectoderm	2.64e-10	173

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
BCL11A#53335	3	28.3694551036071	4.37778126761649e-05	0.000779558564038531
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115657217629035
CHD2#1106	3	10.3440228341169	0.000903370110274688	0.00662456613867281
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327268193281854
E2F4#1874	3	12.6680603152844	0.000491798700629898	0.00438587349458509
EGR1#1958	3	4.98817909481014	0.00805648813738344	0.0322120732200218
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464532748277167
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168202554596145
ETS1#2113	3	9.72876092220234	0.00108584009258484	0.0076453888916246
FOXA1#3169	3	11.0814197493855	0.00073475527569867	0.00583419039296688
GATA3#2625	3	27.236516357206	4.94721007899563e-05	0.00085387815805689
GTF2F1#2962	3	12.7396608767577	0.000483552504743859	0.00435622703725903
IRF1#3659	3	7.6371637535639	0.00224469274729724	0.0128618788519766
MEF2A#4205	2	12.495487273096	0.00823502947802974	0.0324967219699217
MXI1#4601	3	9.9615716287593	0.00101147054125902	0.00722649964827959
MYC#4609	3	5.2222818716094	0.00702084375574015	0.0295772619501329
NANOG#79923	2	19.4965189873418	0.00342725564850102	0.0174604464718926
NFKB1#4790	3	5.48806342419384	0.00604938181565543	0.0270644014498474
NR3C1#2908	3	14.973023331173	0.000297833119467548	0.00309938154285286
PAX5#5079	3	6.66956553117783	0.00337029099967726	0.0173565000845806
PBX3#5090	3	21.9145126867441	9.49854535978121e-05	0.00137284608196816
POU2F2#5452	3	9.10612405774252	0.00132416519268213	0.00885141375822638
POU5F1#5460	2	223.62613430127	2.65611086953324e-05	0.000571961985779757
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.0066761128135948
RFX5#5993	3	12.0479108271951	0.000571724605031258	0.00486319807988757
RXRA#6256	3	20.0746171391333	0.000123573034843222	0.00165842253739287
SIN3A#25942	3	5.40888472681514	0.00631896197799152	0.0277989077514514
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310527315250372
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247656527537021
SP2#6668	3	26.1535304938446	5.58768218891694e-05	0.000942004745969807
TCF12#6938	3	10.6344649021864	0.000831352399020207	0.00631550867044453
TCF7L2#6934	3	10.7701765631373	0.000800318129839838	0.00616813704983712
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0190999770879409
YY1#7528	3	4.91117074985386	0.00844145534180826	0.0330924948178789
ZEB1#6935	3	16.8884320175439	0.000207548691732758	0.00243634683779673

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

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This analysis result is provided for C0 - C305 clusters.