Coexpression cluster:C205

Full id: C205_mycosis_cord_hairy_xeroderma_CD4_B_b

Phase1 CAGE Peaks

Hg19::chr10:110789709..110789714,-	p@chr10:110789709..110789714 -
Hg19::chr10:89577732..89577739,-	p13@ATAD1
Hg19::chr11:118075251..118075262,-	p7@AMICA1
Hg19::chr11:35109970..35109983,+	p@chr11:35109970..35109983 +
Hg19::chr11:35110037..35110046,+	p@chr11:35110037..35110046 +
Hg19::chr11:73720276..73720286,-	p2@UCP3
Hg19::chr12:104319259..104319279,+	p@chr12:104319259..104319279 +
Hg19::chr12:29165730..29165749,-	p@chr12:29165730..29165749 -
Hg19::chr12:39299722..39299767,-	p5@CPNE8
Hg19::chr12:68619488..68619503,-	p3@IL26
Hg19::chr12:68619586..68619593,-	p1@IL26
Hg19::chr12:81172256..81172287,+	p@chr12:81172256..81172287 +
Hg19::chr13:39462565..39462604,-	p@chr13:39462565..39462604 -
Hg19::chr13:40880982..40881019,-	p@chr13:40880982..40881019 -
Hg19::chr13:40881048..40881070,-	p@chr13:40881048..40881070 -
Hg19::chr13:42968329..42968343,+	p@chr13:42968329..42968343 +
Hg19::chr13:50802126..50802138,+	p@chr13:50802126..50802138 +
Hg19::chr14:22355984..22355994,+	p2@TRAV12-2
Hg19::chr14:22356029..22356043,+	p1@TRAV12-2
Hg19::chr14:22356073..22356080,+	p3@TRAV12-2
Hg19::chr14:22356128..22356162,+	p4@TRAV12-2
Hg19::chr14:22356420..22356461,+	p1@AB305742 p1@AF532837 p1@AF532838 p1@AF532839 p1@AF532840 p1@AF532841 p1@AF532842 p1@AF532843 p1@AF532844 p1@AF532845 p1@AF532847 p1@AF532848 p1@AF532849 p1@AF532850 p1@AF532851 p1@AF532852 p1@AF532853 p1@AF532854 p1@AF532856 p1@AY135832 p1@AY135833 p1@AY135834 p1@AY135835 p1@AY135836 p1@AY135837 p1@AY135838 p1@AY135839 p1@AY135840 p1@AY135841 p1@AY135842 p1@AY135843 p1@AY135844 p1@AY135846 p1@AY135847 p1@AY135849 p1@AY135850 p1@AY135851 p1@AY135852 p1@AY135853 p1@EU340840 p1@M17652 p1@M17653 p1@M27369 p1@S82064 p1@X04940 p1@X04946 p1@X92766 p1@X92783 p1@X92883
Hg19::chr14:51651959..51651967,-	p@chr14:51651959..51651967 -
Hg19::chr14:65803148..65803157,+	p@chr14:65803148..65803157 +
Hg19::chr14:65803162..65803174,+	p@chr14:65803162..65803174 +
Hg19::chr14:82495120..82495125,-	p@chr14:82495120..82495125 -
Hg19::chr15:45174767..45174793,-	p@chr15:45174767..45174793 -
Hg19::chr16:10912591..10912602,-	p10@FAM18A
Hg19::chr16:11301790..11301804,+	p1@AK127887
Hg19::chr16:11301814..11301825,+	p2@AK127887
Hg19::chr16:28996572..28996586,+	p6@LAT
Hg19::chr17:32687516..32687555,-	p@chr17:32687516..32687555 -
Hg19::chr17:32690382..32690387,-	p2@CCL1
Hg19::chr17:32690435..32690446,-	p3@CCL1
Hg19::chr18:56816533..56816576,+	p@chr18:56816533..56816576 +
Hg19::chr19:35476657..35476668,+	p@chr19:35476657..35476668 +
Hg19::chr19:35492016..35492027,+	p@chr19:35492016..35492027 +
Hg19::chr19:35492031..35492059,+	p@chr19:35492031..35492059 +
Hg19::chr19:4229557..4229568,+	p1@CU677281
Hg19::chr19:4229572..4229583,+	p2@CU677281
Hg19::chr1:1148422..1148468,-	p@chr1:1148422..1148468 -
Hg19::chr1:1149506..1149515,-	p2@TNFRSF4
Hg19::chr1:1173212..1173215,-	p@chr1:1173212..1173215 -
Hg19::chr1:93043060..93043065,-	p@chr1:93043060..93043065 -
Hg19::chr1:93043102..93043113,-	p@chr1:93043102..93043113 -
Hg19::chr1:93043161..93043170,-	p@chr1:93043161..93043170 -
Hg19::chr1:98642709..98642713,-	p@chr1:98642709..98642713 -
Hg19::chr20:44692500..44692506,-	p@chr20:44692500..44692506 -
Hg19::chr21:36430055..36430067,+	p@chr21:36430055..36430067 +
Hg19::chr21:43826483..43826494,-	p@chr21:43826483..43826494 -
Hg19::chr21:43826497..43826511,-	p@chr21:43826497..43826511 -
Hg19::chr2:160760800..160760805,+	p2@AK125488
Hg19::chr2:53979000..53979012,-	p@chr2:53979000..53979012 -
Hg19::chr3:140980521..140980532,+	p9@ACPL2
Hg19::chr3:16412407..16412418,-	p10@RFTN1
Hg19::chr3:186194261..186194278,+	p1@ENST00000456535
Hg19::chr3:186194280..186194291,+	p2@ENST00000456535
Hg19::chr3:189026010..189026019,+	p@chr3:189026010..189026019 +
Hg19::chr4:2934426..2934445,-	p8@MFSD10
Hg19::chr5:107253874..107253881,-	p@chr5:107253874..107253881 -
Hg19::chr5:107253962..107253972,-	p@chr5:107253962..107253972 -
Hg19::chr5:131541116..131541121,-	p@chr5:131541116..131541121 -
Hg19::chr6:100604462..100604467,-	p@chr6:100604462..100604467 -
Hg19::chr6:128134176..128134183,-	p10@THEMIS
Hg19::chr6:31540488..31540521,+	p2@LTA
Hg19::chr6:31541252..31541272,+	p@chr6:31541252..31541272 +
Hg19::chr6:31541315..31541329,-	p1@CU689955
Hg19::chr7:109650548..109650592,+	p@chr7:109650548..109650592 +
Hg19::chr7:109650713..109650723,+	p@chr7:109650713..109650723 +
Hg19::chr7:142511059..142511075,-	p2@TRBV30
Hg19::chr8:124008167..124008169,+	p@chr8:124008167..124008169 +
Hg19::chr8:29351739..29351773,+	p@chr8:29351739..29351773 +
Hg19::chr8:42037604..42037608,-	p@chr8:42037604..42037608 -
Hg19::chr9:87359709..87359717,+	p@chr9:87359709..87359717 +
Hg19::chr9:92116537..92116544,-	p@chr9:92116537..92116544 -
Hg19::chr9:92116561..92116575,-	p@chr9:92116561..92116575 -
Hg19::chr9:93728939..93728974,-	p@chr9:93728939..93728974 -
Hg19::chr9:93917134..93917162,-	p@chr9:93917134..93917162 -

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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p.value	FDR	nGenes	nPathway	Name
1.21026995633836e-05	0.0076610088236218	4	265	Cytokine-cytokine receptor interaction (KEGG):04060

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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GO ID	GO name	FDR corrected p-value
GO:0006955	immune response	0.000349807746282106
GO:0002376	immune system process	0.000426313808965761
GO:0019722	calcium-mediated signaling	0.00630455178790549
GO:0005125	cytokine activity	0.00973443726723401
GO:0051952	regulation of amine transport	0.0168129406759757
GO:0002036	regulation of L-glutamate transport	0.0168129406759757
GO:0051953	negative regulation of amine transport	0.0168129406759757
GO:0051956	negative regulation of amino acid transport	0.0168129406759757
GO:0002037	negative regulation of L-glutamate transport	0.0168129406759757
GO:0051955	regulation of amino acid transport	0.0168129406759757
GO:0005615	extracellular space	0.0168129406759757
GO:0009605	response to external stimulus	0.0247994292453115
GO:0007267	cell-cell signaling	0.0247994292453115
GO:0046325	negative regulation of glucose import	0.0252186099539889
GO:0048535	lymph node development	0.0271409218658873
GO:0050806	positive regulation of synaptic transmission	0.0271409218658873
GO:0001775	cell activation	0.0271409218658873
GO:0051971	positive regulation of transmission of nerve impulse	0.0271409218658873
GO:0043303	mast cell degranulation	0.0271409218658873
GO:0002448	mast cell mediated immunity	0.0271409218658873
GO:0045576	mast cell activation	0.0271409218658873
GO:0043299	leukocyte degranulation	0.0271409218658873
GO:0046323	glucose import	0.0271409218658873
GO:0046324	regulation of glucose import	0.0271409218658873
GO:0031646	positive regulation of neurological process	0.0271409218658873
GO:0005031	tumor necrosis factor receptor activity	0.0271409218658873
GO:0043525	positive regulation of neuron apoptosis	0.0273704643242504
GO:0002444	myeloid leukocyte mediated immunity	0.0273704643242504
GO:0043120	tumor necrosis factor binding	0.0273704643242504
GO:0044421	extracellular region part	0.027743861225859
GO:0005035	death receptor activity	0.027743861225859
GO:0016021	integral to membrane	0.027743861225859
GO:0031224	intrinsic to membrane	0.027743861225859
GO:0051222	positive regulation of protein transport	0.027743861225859
GO:0019932	second-messenger-mediated signaling	0.027743861225859
GO:0051239	regulation of multicellular organismal process	0.0285894817718104
GO:0045840	positive regulation of mitosis	0.0285894817718104
GO:0006954	inflammatory response	0.028644406585695
GO:0015813	L-glutamate transport	0.028644406585695
GO:0015800	acidic amino acid transport	0.028644406585695
GO:0005102	receptor binding	0.030947997828804
GO:0050804	regulation of synaptic transmission	0.033559563047681
GO:0009612	response to mechanical stimulus	0.0340307536623605
GO:0001772	immunological synapse	0.0340307536623605
GO:0051969	regulation of transmission of nerve impulse	0.0352261380904179
GO:0044459	plasma membrane part	0.0354480104691158
GO:0016020	membrane	0.0372626362680686
GO:0005886	plasma membrane	0.0372626362680686
GO:0044425	membrane part	0.0422303467262425
GO:0045787	positive regulation of progression through cell cycle	0.0422303467262425
GO:0031644	regulation of neurological process	0.0422911808133526
GO:0043523	regulation of neuron apoptosis	0.0422911808133526
GO:0009611	response to wounding	0.0439685993139882
GO:0002274	myeloid leukocyte activation	0.0439685993139882
GO:0051223	regulation of protein transport	0.0447607868065524
GO:0007585	respiratory gaseous exchange	0.0453502471319412
GO:0051402	neuron apoptosis	0.0453502471319412
GO:0015758	glucose transport	0.0453502471319412
GO:0051051	negative regulation of transport	0.0453502471319412
GO:0008645	hexose transport	0.0453502471319412
GO:0015749	monosaccharide transport	0.0453502471319412
GO:0003993	acid phosphatase activity	0.0453502471319412

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>disease_data<br>

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Cell Type

Ontology term	p-value	n
circulating cell	2.22e-59	6
T cell	2.20e-07	25
pro-T cell	2.20e-07	25

Uber Anatomy

Ontology term	p-value	n
umbilical cord	4.37e-36	10
blastocyst	4.37e-36	10
blastula	4.37e-36	10
bilaminar disc	4.37e-36	10
inner cell mass	4.37e-36	10
cleaving embryo	4.37e-36	10
connecting stalk	4.37e-36	10
inner cell mass derived epiblast	4.37e-36	10
extraembryonic mesoderm	4.37e-36	10
blood	2.09e-24	15
haemolymphatic fluid	2.09e-24	15
organism substance	2.09e-24	15
extraembryonic structure	1.31e-15	24

Disease

Ontology term	p-value	n
non-Hodgkin lymphoma	6.62e-41	1
cutaneous T cell lymphoma	6.62e-41	1
mycosis fungoides	6.62e-41	1

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
BATF#10538	12	3.74735412189287	7.91095060496588e-05	0.00121198734081272
BCL11A#53335	9	3.27339866580081	0.00169969319151139	0.0106175164320987

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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