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UBERON:0000029

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Name:lymph node
Namespace:FANTOM
Definition:"Oval or bean shaped bodies (1 - 30 mm in diameter) located along the lymphatic system. Lymph nodes are garrisons of B, T, and other immune cells. Lymph nodes are found all through the body, and act as filters or traps for foreign particles. They contain white blood cells that use oxygen to process. Thus they are important in the proper functioning of the immune system. The lymph node is surrounded by a fibrous capsule, and inside the lymph node the fibrous capsule extends to form trabeculae. The substance of the lymph node is divided into the outer cortex and the inner medulla surrounded by the former all around except for at the hilum, where the medulla comes in direct contact with the surface. Thin reticular fibers, elastin and reticular fibers form a supporting meshwork called reticular network (RN) inside the node, within which the white blood cells (WBCs), most prominently, lymphocytes are tightly packed as follicles in the cortex. Elsewhere, there are only occasional WBCs. The RN provides not just the structural support, but also provide surface for adhesion of the dendritic cells, macrophages and lymphocytes. It allows for exchange of material with blood through the high endothelial venules and provides the growth and regulatory factors necessary for activation and maturation of immune cells[WP]." [GAID:947, Wikipedia:Lymph_node]
Xrefs:
links:

BTO:0000784
EFO:0000872
EV:0100050
FMA:5034
GAID:947
galen:Lymphnode
[ Illu_lymph_node_structure.png Illu_lymph_node_structure.png]
MA:0000139
MAT:0000442
MESH:A.15.382.520.604.412
ncithesaurus:Lymph_Node
OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA
SCTID:181756000
TAO:0005318
VHOG:0001273

ZFA:0005318
Synonyms: "nodus lymphaticus" RELATED LATIN [Wikipedia:Lymph_node]
Subset: uberon_slim
vertebrate_core

Ontology association
Each term has an is_a parent in the Uberon Ontology, which has a linkage to an another entity and FANTOM5 samples.Libraries were grouped into mutually exclusive facets according to the FANTOM5 sample ontology mapping to UBERON ontologies.

link to ontology dataset
data


Parents

is_a:UBERON:0005057(immune organ)
part_of:UBERON:0002465(lymphoid system)



Children

is a:UBERON:0003968 (peripheral lymph node)
derives from:FF:0010077 (human lymph node - adult sample)

Ontology Tree: Loaded from BioPortal


FF samples
It includes FANTOM5 samples that overlay the Uberon ontology


Human (Homo sapiens)

Mouse (Mus musculus)


Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0000029 (lymph node), sorted by p-values
Analyst: Hideya Kawaji

link to source dataset
human : data
mouse : data


P-valueFFCPShort description
3.07e-86FFCP PHASE1:Mm9::chr8:3918216..3918219,-#_9fc0d38988654f20bcd3d8b238a70250p@chr8:3918216..3918219, -
3.07e-86FFCP PHASE1:Mm9::chr16:19235714..19235723,-#_9fc0d38988654f20bcd3d8b238a70250p@chr16:19235714..19235723, -
3.07e-86FFCP PHASE2:Mm9::chr4:122604700..122604706,-#_9fc0d38988654f20bcd3d8b238a70250p@chr4:122604700..122604706, -
3.07e-86FFCP PHASE2:Mm9::chr15:98457062..98457072,+#_9fc0d38988654f20bcd3d8b238a70250p@chr15:98457062..98457072, +
3.07e-86FFCP PHASE1:Mm9::chr12:104978425..104978430,-#_9fc0d38988654f20bcd3d8b238a70250p@chr12:104978425..104978430, -
3.07e-86FFCP PHASE1:Mm9::chr11:5405967..5405985,+#_9fc0d38988654f20bcd3d8b238a70250p@chr11:5405967..5405985, +
3.07e-86FFCP PHASE1:Mm9::chr12:93042811..93042816,-#_9fc0d38988654f20bcd3d8b238a70250p@chr12:93042811..93042816, -
3.07e-86FFCP PHASE1:Mm9::chr4:122604700..122604706,-#_9fc0d38988654f20bcd3d8b238a70250p@chr4:122604700..122604706, -
3.07e-86FFCP PHASE1:Mm9::chr10:73409774..73409819,+#_9fc0d38988654f20bcd3d8b238a70250p@chr10:73409774..73409819, +
3.07e-86FFCP PHASE2:Mm9::chr15:98457111..98457118,+#_9fc0d38988654f20bcd3d8b238a70250p@chr15:98457111..98457118, +
3.07e-86FFCP PHASE1:Mm9::chr4:32325858..32325865,+#_9fc0d38988654f20bcd3d8b238a70250p18@Bach2
3.07e-86FFCP PHASE1:Mm9::chr15:98457062..98457072,+#_9fc0d38988654f20bcd3d8b238a70250p@chr15:98457062..98457072, +
3.07e-86FFCP PHASE2:Mm9::chr8:3918216..3918219,-#_9fc0d38988654f20bcd3d8b238a70250p@chr8:3918216..3918219, -
3.07e-86FFCP PHASE1:Mm9::chr17:37383896..37383899,+#_9fc0d38988654f20bcd3d8b238a70250p2@ENSMUST00000172477
3.07e-86FFCP PHASE2:Mm9::chr12:93042811..93042816,-#_9fc0d38988654f20bcd3d8b238a70250p@chr12:93042811..93042816, -
3.07e-86FFCP PHASE2:Mm9::chr10:73409774..73409819,+#_9fc0d38988654f20bcd3d8b238a70250p@chr10:73409774..73409819, +
3.07e-86FFCP PHASE1:Mm9::chr15:98457111..98457118,+#_9fc0d38988654f20bcd3d8b238a70250p@chr15:98457111..98457118, +
3.07e-86FFCP PHASE1:Mm9::chr12:114567506..114567507,-#_9fc0d38988654f20bcd3d8b238a70250p@chr12:114567506..114567507, -
3.07e-86FFCP PHASE2:Mm9::chr12:104978425..104978430,-#_9fc0d38988654f20bcd3d8b238a70250p@chr12:104978425..104978430, -
3.07e-86FFCP PHASE2:Mm9::chr4:32325858..32325865,+#_9fc0d38988654f20bcd3d8b238a70250p18@Bach2
3.07e-86FFCP PHASE2:Mm9::chr16:19235714..19235723,-#_9fc0d38988654f20bcd3d8b238a70250p@chr16:19235714..19235723, -
3.07e-86FFCP PHASE2:Mm9::chr11:5405967..5405985,+#_9fc0d38988654f20bcd3d8b238a70250p@chr11:5405967..5405985, +
3.07e-86FFCP PHASE2:Mm9::chr17:37383896..37383899,+#_9fc0d38988654f20bcd3d8b238a70250p2@ENSMUST00000172477
3.07e-86FFCP PHASE2:Mm9::chr12:114567506..114567507,-#_9fc0d38988654f20bcd3d8b238a70250p@chr12:114567506..114567507, -
2.39e-66FFCP PHASE2:Hg19::chr5:99385820..99385831,-#_4f60b1b271c4a1c975e9f2d38c9fdcf9p@chr5:99385820..99385831, -
2.39e-66FFCP PHASE1:Hg19::chr5:99385820..99385831,-#_4f60b1b271c4a1c975e9f2d38c9fdcf9p@chr5:99385820..99385831, -
4.66e-66FFCP PHASE1:Hg19::chr4:146461014..146461025,+#_fb6569494edf7e83993220d56a3bc320p@chr4:146461014..146461025, +
4.66e-66FFCP PHASE2:Hg19::chr4:146461014..146461025,+#_fb6569494edf7e83993220d56a3bc320p@chr4:146461014..146461025, +
1.46e-50FFCP PHASE1:Hg19::chr20:3687858..3687862,-#_efdd99588b88a5759232c1dd715ba866p1@SIGLEC1
1.46e-50FFCP PHASE1:Hg19::chr14:107034971..107034980,-#_efdd99588b88a5759232c1dd715ba866p1@AM279543, p1@AY577299, p1@FJ385326, p1@GQ232913, p1@GQ232958, p1@GU552732, p1@GU552750, p1@S73611, p1@S73613
1.46e-50FFCP PHASE2:Hg19::chr20:3687858..3687862,-#_efdd99588b88a5759232c1dd715ba866p1@SIGLEC1
1.46e-50FFCP PHASE2:Hg19::chr14:107034971..107034980,-#_efdd99588b88a5759232c1dd715ba866p1@AM279543, p1@AY577299, p1@FJ385326, p1@GQ232913, p1@GQ232958, p1@GU552732, p1@GU552750, p1@S73611, p1@S73613
2.42e-50FFCP PHASE1:Hg19::chr2:68582248..68582253,-#_14f2586ac5c89fb5e4b7137ce7694b86p@chr2:68582248..68582253, -
2.42e-50FFCP PHASE2:Hg19::chr2:68582248..68582253,-#_14f2586ac5c89fb5e4b7137ce7694b86p@chr2:68582248..68582253, -
2.42e-50FFCP PHASE2:Hg19::chr14:106237005..106237028,+#_14f2586ac5c89fb5e4b7137ce7694b86p@chr14:106237005..106237028, +
2.42e-50FFCP PHASE1:Hg19::chr14:106237005..106237028,+#_14f2586ac5c89fb5e4b7137ce7694b86p@chr14:106237005..106237028, +
3.99e-50FFCP PHASE1:Hg19::chr12:57038878..57038884,-#_d9f588e777a059f01e98519a4ad5da5cp1@SNORD59A
3.99e-50FFCP PHASE2:Hg19::chr12:57038878..57038884,-#_d9f588e777a059f01e98519a4ad5da5cp1@SNORD59A
3.99e-50FFCP PHASE2:Hg19::chr14:106091539..106091550,-#_d9f588e777a059f01e98519a4ad5da5cp@chr14:106091539..106091550, -
3.99e-50FFCP PHASE1:Hg19::chr14:106091539..106091550,-#_d9f588e777a059f01e98519a4ad5da5cp@chr14:106091539..106091550, -
6.58e-50FFCP PHASE1:Hg19::chr1:22974264..22974270,+#_a90cc1ca10b272b63226d43f0f624583p@chr1:22974264..22974270, +
6.58e-50FFCP PHASE1:Hg19::chr2:103043089..103043100,+#_a90cc1ca10b272b63226d43f0f624583p@chr2:103043089..103043100, +
6.58e-50FFCP PHASE1:Hg19::chr14:106725293..106725299,-#_a90cc1ca10b272b63226d43f0f624583p1@AF460806, p1@DQ523922
6.58e-50FFCP PHASE2:Hg19::chr14:106725293..106725299,-#_a90cc1ca10b272b63226d43f0f624583p1@AF460806, p1@DQ523922
6.58e-50FFCP PHASE1:Hg19::chr1:40847015..40847027,+#_a90cc1ca10b272b63226d43f0f624583p@chr1:40847015..40847027, +
6.58e-50FFCP PHASE2:Hg19::chr18:514455..514467,+#_a90cc1ca10b272b63226d43f0f624583p@chr18:514455..514467, +
6.58e-50FFCP PHASE2:Hg19::chr2:103043089..103043100,+#_a90cc1ca10b272b63226d43f0f624583p@chr2:103043089..103043100, +
6.58e-50FFCP PHASE1:Hg19::chr18:514455..514467,+#_a90cc1ca10b272b63226d43f0f624583p@chr18:514455..514467, +
6.58e-50FFCP PHASE2:Hg19::chr1:40847015..40847027,+#_a90cc1ca10b272b63226d43f0f624583p@chr1:40847015..40847027, +
6.58e-50FFCP PHASE2:Hg19::chr1:22974264..22974270,+#_a90cc1ca10b272b63226d43f0f624583p@chr1:22974264..22974270, +
2.74e-44FFCP PHASE2:Mm9::chr2:152582794..152582807,+#_24cb5bc3ebc4e6cf97687e83968266ccp@chr2:152582794..152582807, +
2.74e-44FFCP PHASE1:Mm9::chr4:130488147..130488154,+#_24cb5bc3ebc4e6cf97687e83968266ccp@chr4:130488147..130488154, +
2.74e-44FFCP PHASE2:Mm9::chr6:129628862..129628871,-#_24cb5bc3ebc4e6cf97687e83968266ccp@chr6:129628862..129628871, -
2.74e-44FFCP PHASE1:Mm9::chr6:129628862..129628871,-#_24cb5bc3ebc4e6cf97687e83968266ccp@chr6:129628862..129628871, -
2.74e-44FFCP PHASE2:Mm9::chr3:87316559..87316571,-#_24cb5bc3ebc4e6cf97687e83968266ccp@chr3:87316559..87316571, -
2.74e-44FFCP PHASE2:Mm9::chr4:130488147..130488154,+#_24cb5bc3ebc4e6cf97687e83968266ccp@chr4:130488147..130488154, +
2.74e-44FFCP PHASE1:Mm9::chr3:87316559..87316571,-#_24cb5bc3ebc4e6cf97687e83968266ccp@chr3:87316559..87316571, -
2.74e-44FFCP PHASE2:Mm9::chr6:127022920..127022928,+#_24cb5bc3ebc4e6cf97687e83968266ccp1@Fgf23
2.74e-44FFCP PHASE1:Mm9::chr15:100610674..100610678,+#_24cb5bc3ebc4e6cf97687e83968266ccp@chr15:100610674..100610678, +
2.74e-44FFCP PHASE2:Mm9::chr1:156901987..156901994,-#_24cb5bc3ebc4e6cf97687e83968266ccp@chr1:156901987..156901994, -
2.74e-44FFCP PHASE2:Mm9::chr15:100610674..100610678,+#_24cb5bc3ebc4e6cf97687e83968266ccp@chr15:100610674..100610678, +
2.74e-44FFCP PHASE1:Mm9::chr2:152582794..152582807,+#_24cb5bc3ebc4e6cf97687e83968266ccp@chr2:152582794..152582807, +
2.74e-44FFCP PHASE1:Mm9::chr1:156901987..156901994,-#_24cb5bc3ebc4e6cf97687e83968266ccp@chr1:156901987..156901994, -
2.74e-44FFCP PHASE1:Mm9::chr6:127022920..127022928,+#_24cb5bc3ebc4e6cf97687e83968266ccp1@Fgf23
7.47e-44FFCP PHASE1:Mm9::chr8:22042143..22042150,-#_e64ead76e727cf365aabca81eaca0ccap1@Gm15056, p1@LOC100504014
7.47e-44FFCP PHASE1:Mm9::chr13:83714297..83714301,+#_e64ead76e727cf365aabca81eaca0cca+, p@chr13:83714297..83714301
7.47e-44FFCP PHASE2:Mm9::chr1:69594451..69594464,-#_e64ead76e727cf365aabca81eaca0ccap@chr1:69594451..69594464, -
7.47e-44FFCP PHASE1:Mm9::chr17:73506745..73506750,+#_e64ead76e727cf365aabca81eaca0ccap@chr17:73506745..73506750, +
7.47e-44FFCP PHASE2:Mm9::chr17:73506745..73506750,+#_e64ead76e727cf365aabca81eaca0ccap@chr17:73506745..73506750, +
7.47e-44FFCP PHASE1:Mm9::chr5:111607677..111607689,-#_e64ead76e727cf365aabca81eaca0ccap@chr5:111607677..111607689, -
7.47e-44FFCP PHASE2:Mm9::chr2:26524291..26524300,-#_e64ead76e727cf365aabca81eaca0ccap@chr2:26524291..26524300, -
7.47e-44FFCP PHASE2:Mm9::chr8:22042143..22042150,-#_e64ead76e727cf365aabca81eaca0ccap1@Gm15056, p1@LOC100504014
7.47e-44FFCP PHASE1:Mm9::chr2:70769189..70769223,+#_e64ead76e727cf365aabca81eaca0ccap@chr2:70769189..70769223, +
7.47e-44FFCP PHASE1:Mm9::chr1:156901880..156901891,-#_e64ead76e727cf365aabca81eaca0cca-, p@chr1:156901880..156901891
7.47e-44FFCP PHASE2:Mm9::chrX:7157626..7157635,+#_e64ead76e727cf365aabca81eaca0ccap3@Foxp3
7.47e-44FFCP PHASE2:Mm9::chr13:83714297..83714301,+#_e64ead76e727cf365aabca81eaca0ccap@chr13:83714297..83714301, +
7.47e-44FFCP PHASE1:Mm9::chr2:26524291..26524300,-#_e64ead76e727cf365aabca81eaca0ccap@chr2:26524291..26524300, -
7.47e-44FFCP PHASE2:Mm9::chr17:73460572..73460579,+#_e64ead76e727cf365aabca81eaca0ccap@chr17:73460572..73460579, +
7.47e-44FFCP PHASE2:Mm9::chr2:70769189..70769223,+#_e64ead76e727cf365aabca81eaca0ccap@chr2:70769189..70769223, +
7.47e-44FFCP PHASE2:Mm9::chrX:13200511..13200521,+#_e64ead76e727cf365aabca81eaca0ccap@chrX:13200511..13200521, +
7.47e-44FFCP PHASE1:Mm9::chrX:13200511..13200521,+#_e64ead76e727cf365aabca81eaca0ccap@chrX:13200511..13200521, +
7.47e-44FFCP PHASE2:Mm9::chr5:111607677..111607689,-#_e64ead76e727cf365aabca81eaca0ccap@chr5:111607677..111607689, -
7.47e-44FFCP PHASE1:Mm9::chrX:7157626..7157635,+#_e64ead76e727cf365aabca81eaca0ccap3@Foxp3
7.47e-44FFCP PHASE2:Mm9::chr1:156901880..156901891,-#_e64ead76e727cf365aabca81eaca0ccap@chr1:156901880..156901891, -
7.47e-44FFCP PHASE1:Mm9::chr17:73460572..73460579,+#_e64ead76e727cf365aabca81eaca0ccap@chr17:73460572..73460579, +
7.47e-44FFCP PHASE1:Mm9::chr1:69594451..69594464,-#_e64ead76e727cf365aabca81eaca0ccap@chr1:69594451..69594464, -
1.48e-40FFCP PHASE2:Hg19::chr14:106321813..106321821,+#_51069257db7e761178c4295cd3423846p5@AY671148, p5@AY671772, p5@AY671782, p5@AY671783
1.48e-40FFCP PHASE1:Hg19::chr4:109000758..109000770,-#_51069257db7e761178c4295cd3423846p49@LEF1
1.48e-40FFCP PHASE1:Hg19::chr14:106321813..106321821,+#_51069257db7e761178c4295cd3423846p5@AY671148, p5@AY671772, p5@AY671782, p5@AY671783
1.48e-40FFCP PHASE2:Hg19::chr4:109000758..109000770,-#_51069257db7e761178c4295cd3423846p49@LEF1
2.21e-40FFCP PHASE2:Hg19::chr6:109669625..109669629,+#_ccac7fdf41f11a5289a9d2eda43c1bb1p@chr6:109669625..109669629, +
2.21e-40FFCP PHASE2:Hg19::chr15:31685082..31685093,+#_ccac7fdf41f11a5289a9d2eda43c1bb1p40@KLF13
2.21e-40FFCP PHASE1:Hg19::chr6:109669625..109669629,+#_ccac7fdf41f11a5289a9d2eda43c1bb1p@chr6:109669625..109669629, +
2.21e-40FFCP PHASE1:Hg19::chr15:31685082..31685093,+#_ccac7fdf41f11a5289a9d2eda43c1bb1p40@KLF13
2.21e-40FFCP PHASE1:Hg19::chr17:6983503..6983512,-#_ccac7fdf41f11a5289a9d2eda43c1bb1p5@CLEC10A
2.21e-40FFCP PHASE2:Hg19::chr17:6983503..6983512,-#_ccac7fdf41f11a5289a9d2eda43c1bb1p5@CLEC10A
2.58e-34FFCP PHASE2:Hg19::chr2:28824788..28824791,+#_94a97a7ce0533e4ed712be682d9cd2e0p7@PLB1
2.58e-34FFCP PHASE1:Hg19::chr2:207082631..207082640,-#_94a97a7ce0533e4ed712be682d9cd2e0p7@GPR1
2.58e-34FFCP PHASE2:Hg19::chr2:207082631..207082640,-#_94a97a7ce0533e4ed712be682d9cd2e0p7@GPR1
2.58e-34FFCP PHASE1:Hg19::chr2:28824788..28824791,+#_94a97a7ce0533e4ed712be682d9cd2e0p7@PLB1