Coexpression cluster:C867

Full id: C867_CD4_CD8_Natural_CD19_Peripheral_cerebellum_Mast

Phase1 CAGE Peaks

Hg19::chr10:114206689..114206719,-	p2@ZDHHC6
Hg19::chr12:133562945..133562958,+	p2@ZNF26
Hg19::chr16:20753114..20753157,-	p1@THUMPD1
Hg19::chr19:12273866..12273935,+	p1@ZNF136
Hg19::chr19:19843900..19843928,-	p1@ZNF14
Hg19::chr1:114354876..114354922,-	p1@RSBN1
Hg19::chr3:3221368..3221391,-	p1@CRBN
Hg19::chr4:68411182..68411240,-	p1@CENPC1
Hg19::chr5:78531917..78531974,+	p1@JMY

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
hematopoietic stem cell	1.39e-27	172
angioblastic mesenchymal cell	1.39e-27	172
leukocyte	5.10e-26	140
hematopoietic oligopotent progenitor cell	2.89e-24	165
hematopoietic multipotent progenitor cell	2.89e-24	165
hematopoietic cell	2.49e-23	182
hematopoietic lineage restricted progenitor cell	2.22e-19	124
nongranular leukocyte	1.16e-17	119
lymphoid lineage restricted progenitor cell	1.60e-15	52
lymphocyte	2.59e-15	53
common lymphoid progenitor	2.59e-15	53
mature alpha-beta T cell	1.17e-11	18
alpha-beta T cell	1.17e-11	18
immature T cell	1.17e-11	18
mature T cell	1.17e-11	18
immature alpha-beta T cell	1.17e-11	18
myeloid cell	2.05e-10	112
common myeloid progenitor	2.05e-10	112
T cell	6.98e-09	25
pro-T cell	6.98e-09	25
CD8-positive, alpha-beta T cell	3.58e-08	11
myeloid leukocyte	5.04e-08	76
B cell	2.16e-07	14

Uber Anatomy

Ontology term	p-value	n
adult organism	1.13e-34	115
neural tube	1.94e-16	57
neural rod	1.94e-16	57
future spinal cord	1.94e-16	57
neural keel	1.94e-16	57
anterior neural tube	4.67e-15	42
regional part of forebrain	7.85e-15	41
forebrain	7.85e-15	41
future forebrain	7.85e-15	41
central nervous system	4.58e-14	82
regional part of nervous system	2.55e-13	94
nervous system	2.55e-13	94
regional part of brain	1.08e-12	59
brain	1.94e-12	69
future brain	1.94e-12	69
gray matter	7.91e-12	34
brain grey matter	7.91e-12	34
telencephalon	9.82e-12	34
regional part of telencephalon	2.04e-11	33
cerebral hemisphere	4.38e-11	32
regional part of cerebral cortex	3.05e-09	22
neurectoderm	4.25e-09	90
hematopoietic system	7.19e-09	102
blood island	7.19e-09	102
neural plate	1.37e-08	86
presumptive neural plate	1.37e-08	86
neocortex	1.82e-08	20
cerebral cortex	1.96e-08	25
pallium	1.96e-08	25
hemolymphoid system	3.38e-07	112
pre-chordal neural plate	7.12e-07	61

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
ATF3#467	3	7.48772484200292	0.00605035742055281	0.0268399642630555
BCLAF1#9774	3	7.21754920337395	0.0067040496194776	0.028500192868833
BRCA1#672	5	11.2134614684576	3.17534800280252e-05	0.000637505132765653
CCNT2#905	6	4.22413438464176	0.00084033506380825	0.00633719068012635
CHD2#1106	6	6.89601522274457	5.28898897155739e-05	0.000897443897969914
E2F1#1869	8	4.3621237465594	2.18983367577486e-05	0.000480874767166213
E2F6#1876	8	4.45969398373101	1.843503537119e-05	0.000418915722178353
ELF1#1997	9	4.25809795880754	2.17161853202127e-06	7.81805128803066e-05
ETS1#2113	6	6.48584061480156	7.51193928811803e-05	0.001163142219884
FOXA2#3170	3	8.21015458422175	0.0046728123675689	0.0220505987193443
GABPB1#2553	6	4.71178922412145	0.000457630704900798	0.00421691311003481
GATA1#2623	4	6.02680361946686	0.00275314489424295	0.0150992858063246
GTF2F1#2962	4	5.66207150078118	0.0034642002070655	0.0176005840351096
HEY1#23462	9	4.04011104310571	3.4850025352467e-06	0.000115914069993194
HMGN3#9324	5	4.54363762408366	0.00224461831902441	0.0128897395183697
IRF1#3659	7	5.94001625277192	1.86166156219947e-05	0.000422765974982714
MXI1#4601	4	4.42736516833747	0.00844465741513493	0.0327753382057779
MYC#4609	7	4.06177478902954	0.000235555679657337	0.00256717099318926
NFKB1#4790	8	4.87827859928341	9.15949022225393e-06	0.000244469205040117
NFYA#4800	3	6.14186023327684	0.0104816316305809	0.0388133288138647
NFYB#4801	3	5.58659775117882	0.0135850027711194	0.0479455293462062
NRF1#4899	7	9.49688401488626	7.65865712776971e-07	3.36359332114021e-05
PAX5#5079	7	5.18743985758276	4.62776729125731e-05	0.000812301492658189
POLR2A#5430	9	2.14745317655807	0.00102941289260802	0.00728294628716227
POU2F2#5452	6	6.07074937182835	0.000109527229587528	0.00152336054479849
SETDB1#9869	3	13.4400087260035	0.00114472325146679	0.0078365070568917
SIN3A#25942	8	4.80789753494679	1.02597602607548e-05	0.000267879775468243
SIX5#147912	5	9.49261964192167	7.08068365528068e-05	0.00111757521576826
SP1#6667	5	3.1657674323005	0.0111972168609182	0.0411176165302709
SRF#6722	5	7.66509903453767	0.000196444781216345	0.00236120341874253
TAF1#6872	9	3.34304628574529	1.91655056102793e-05	0.000433252432993932
TAF7#6879	4	5.08136417996618	0.0051419296120382	0.0239035870538439
TBP#6908	9	3.70677068709639	7.56501052505806e-06	0.000215869435581021
TCF7L2#6934	5	5.98343142396519	0.000630515439732144	0.00518343844538613
TRIM28#10155	4	8.26245557567223	0.000846928597179193	0.00638322694384049
USF1#7391	5	3.53416626511553	0.0069229675408181	0.0293079775839279
YY1#7528	8	4.36548511098121	2.17675027117712e-05	0.000478907987300331
ZNF143#7702	4	6.00038957876796	0.00279812872640546	0.0153210530595082
ZNF263#10127	5	4.56768979833926	0.00219130580900913	0.012632909438458

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.