Personal tools

UBERON:0004208: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{UBERON |id=UBERON:0004208 |name=nephrogenic mesenchyme |namespace= |def="Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephr...")
 
No edit summary
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{UBERON
{{UBERON
|id=UBERON:0004208
|name=nephrogenic mesenchyme
|namespace=
|def="Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron" [GO:0072076]
|xref=
|is_a=UBERON:0003104
|synonym="mesenchyme of nephron" EXACT [OBOL:automatic];;"nephron mesenchyme" EXACT [OBOL:automatic]
|comment=The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman窶冱 capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman窶冱 capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman窶冱 capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]
|alt_id=
|alt_id=
|disjoint_from=
|comment=The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman遯ｶ蜀ｱ capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman遯ｶ蜀ｱ capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman遯ｶ蜀ｱ capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [http://www.gudmap.org/About/Tutorial/DevMUS.html#DMK_Nephron]
|union_of=
|created_by=
|created_by=
|obo_creation_date=
|def="Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron" [GO:0072076]
|subset=
|adjacent_to=
|derives_from=
|derives_from=
|develops_from=
|develops_from=
|disjoint_from=
|has_quality=
|has_quality=
|id=UBERON:0004208
|is_a=UBERON:0003104
|is_obsolete=
|located_in=
|located_in=
|name=nephrogenic mesenchyme
|namespace=FANTOM
|obo_creation_date=
|part_of=
|part_of=
|preceded_by=
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|property_value=IAO:0000412 http://purl.obolibrary.org/obo/uberon.owl
|subset=
|synonym="mesenchyme of nephron" EXACT [OBOL:automatic];;"nephron mesenchyme" EXACT [OBOL:automatic]
|union_of=
|xref=
}}
}}

Latest revision as of 17:45, 12 September 2014

Name:nephrogenic mesenchyme
Namespace:FANTOM
Definition:"Nephrogenic mesenchyme is the tissue made up of loosely connected mesenchymal cells in the nephron" [GO:0072076]
Synonyms: "mesenchyme of nephron" EXACT [OBOL:automatic]
"nephron mesenchyme" EXACT [OBOL:automatic]
Comments:The detailed events associated with the differentiation of the nephrogenic mesenchyme are somewhat complex. It has been suggested that each terminal branch of the ureteric bud stimulates the associated cap mesenchyme tissue to form a renal vesicle (the most primitive stage of nephron development: a stage I nephron). This then elongates, becomes a comma-shaped and then an S-shaped body (stage II nephron), and makes contact with and fuses with the distal component of the ureteric bud. The latter then forms the collecting duct. One fold of the S-shaped body gives rise to Bowman遯ｶ蜀ｱ capsule (also termed the glomerular capsule). Soon afterwards, endothelial cells invade to make a capillary knot-like outgrowth, the glomerular tuft, which goes on to form the glomerulus. The inner epithelial layer of the Bowman遯ｶ蜀ｱ capsule (also called the visceral epithelium, or podocyte layer because it consists of podocytes) is closely apposed to the endothelial glomerulus. Together, the Bowman遯ｶ蜀ｱ capsule and the glomerulus comprise the definitive renal corpuscle. The rest of the nephron elongates to form components of the proximal tubule, the loop of Henle and the distal tubule. The distal pole of the developing nephron connects to the ureteric bud that induced it at an early stage of nephron/ collecting duct development, before differentiation of the proximal tubule, the loop of Henle and the distal tubule are complete. This connection allows the excretory products produced by the kidney to be removed and subsequently transferred, via the ureter, into the bladder where they are stored until it is appropriate to empty the bladder. [1]

Ontology association<br>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.<br><br>link to ontology dataset<br>data

Parents

is_a:UBERON:0003104(mesenchyme)



Children

develops from:UBERON:0001285 (nephron),UBERON:0004209 (renal vesicle)

Ontology Tree: Loaded from BioPortal

Ontorolgy tree(Small window open)

FF samples<br>It includes FANTOM5 samples that overlay the Uberon ontology



Enrichment analysis: top 100 FFCP enriched with this ontology term TOP 100 FANTOM5 Cage Peaks enriched with UBERON:0004208 (nephrogenic mesenchyme), sorted by p-values <br>Analyst: Hideya Kawaji<br><br>link to source dataset <br>human : data <br>mouse : data

P-valueFFCPShort description
1.05e-87FFCP PHASE2:Hg19::chr2:693380..693398,+#_d9e6b5011f13871310731e58ab649952p@chr2:693380..693398, +
1.05e-87FFCP PHASE1:Hg19::chr2:693380..693398,+#_d9e6b5011f13871310731e58ab649952p@chr2:693380..693398, +
1.72e-83FFCP PHASE1:Hg19::chr15:66420804..66420837,-#_4da43d476d3f844cd6217d666a2883fep4@MEGF11
1.72e-83FFCP PHASE2:Hg19::chr15:66420804..66420837,-#_4da43d476d3f844cd6217d666a2883fep4@MEGF11
2.2e-74FFCP PHASE1:Hg19::chr7:27219833..27219845,-#_6dc97beafc1c66ea806d13b261150008p7@HOXA10
2.2e-74FFCP PHASE2:Hg19::chr7:27219833..27219845,-#_6dc97beafc1c66ea806d13b261150008p7@HOXA10
7.63e-66FFCP PHASE2:Hg19::chr1:1100457..1100470,+#_73f010210c7ed389a8e20dbd1b99499dp@chr1:1100457..1100470, +
7.63e-66FFCP PHASE1:Hg19::chr1:1100457..1100470,+#_73f010210c7ed389a8e20dbd1b99499dp@chr1:1100457..1100470, +
6.44e-62FFCP PHASE2:Hg19::chr10:102495147..102495159,+#_3343a9878a55dff1388b7e2059ba26eap4@PAX2
6.44e-62FFCP PHASE1:Hg19::chr10:102495147..102495159,+#_3343a9878a55dff1388b7e2059ba26eap4@PAX2
5.84e-60FFCP PHASE2:Hg19::chr18:3456189..3456200,+#_1a36de97e867e27867ea9a7a2fae5135p@chr18:3456189..3456200, +
5.84e-60FFCP PHASE1:Hg19::chr18:3456189..3456200,+#_1a36de97e867e27867ea9a7a2fae5135p@chr18:3456189..3456200, +
6.18e-60FFCP PHASE2:Hg19::chr10:102505954..102505973,+#_7ccea358c3c775d8c7dde23811f522d0p3@PAX2
6.18e-60FFCP PHASE1:Hg19::chr10:102505954..102505973,+#_7ccea358c3c775d8c7dde23811f522d0p3@PAX2
4.45e-59FFCP PHASE1:Hg19::chr20:6034607..6034616,-#_ec94d1d167d34384f85ca2afe0bf7820p6@LRRN4
4.45e-59FFCP PHASE2:Hg19::chr20:6034607..6034616,-#_ec94d1d167d34384f85ca2afe0bf7820p6@LRRN4
3.49e-58FFCP PHASE2:Hg19::chr5:74244100..74244117,+#_0d4c331dbdfb5a59054c50b7142b0776p@chr5:74244100..74244117, +
3.49e-58FFCP PHASE1:Hg19::chr5:74244100..74244117,+#_0d4c331dbdfb5a59054c50b7142b0776p@chr5:74244100..74244117, +
3.91e-56FFCP PHASE1:Hg19::chr20:6033532..6033548,-#_cc0e391df52ec627d78e0e5c0e3d1c8ep2@AB527789
3.91e-56FFCP PHASE2:Hg19::chr20:6033532..6033548,-#_cc0e391df52ec627d78e0e5c0e3d1c8ep2@AB527789
3.83e-55FFCP PHASE2:Hg19::chr16:86604624..86604648,+#_e8d55f8846658aaa324bd17e31ae1b50p@chr16:86604624..86604648, +
3.83e-55FFCP PHASE1:Hg19::chr16:86604624..86604648,+#_e8d55f8846658aaa324bd17e31ae1b50p@chr16:86604624..86604648, +
3.51e-54FFCP PHASE1:Hg19::chr16:86768403..86768437,+#_4ffb678b748199ae386f39ecbf4ebea5p@chr16:86768403..86768437, +
3.51e-54FFCP PHASE2:Hg19::chr16:86768403..86768437,+#_4ffb678b748199ae386f39ecbf4ebea5p@chr16:86768403..86768437, +
6.09e-53FFCP PHASE1:Hg19::chr16:3068288..3068312,-#_a2829cd1b266ce4c6d07e4d8e7aca237p2@CLDN6
6.09e-53FFCP PHASE2:Hg19::chr16:3068288..3068312,-#_a2829cd1b266ce4c6d07e4d8e7aca237p2@CLDN6
2.79e-52FFCP PHASE2:Hg19::chr1:81001398..81001426,+#_a9cc0be51fb7933b63bc4d32f76b6b34p1@ENST00000418041, p1@ENST00000443104
2.79e-52FFCP PHASE1:Hg19::chr1:81001398..81001426,+#_a9cc0be51fb7933b63bc4d32f76b6b34p1@ENST00000418041, p1@ENST00000443104
1.61e-50FFCP PHASE2:Hg19::chr7:7606139..7606151,-#_6c206fd8575085b6f294ebfd22325bedp@chr7:7606139..7606151, -
1.61e-50FFCP PHASE1:Hg19::chr7:7606139..7606151,-#_6c206fd8575085b6f294ebfd22325bedp@chr7:7606139..7606151, -
1.96e-50FFCP PHASE1:Hg19::chr17:36104873..36104903,-#_4c6c388fdd0da81c3644fb5f05708fb4p3@HNF1B
1.96e-50FFCP PHASE2:Hg19::chr17:36104873..36104903,-#_4c6c388fdd0da81c3644fb5f05708fb4p3@HNF1B
1.73e-49FFCP PHASE2:Hg19::chr7:140227349..140227360,-#_70638d20b538b6aab1b6a8092bb22b98p@chr7:140227349..140227360, -
1.73e-49FFCP PHASE1:Hg19::chr7:140227349..140227360,-#_70638d20b538b6aab1b6a8092bb22b98p@chr7:140227349..140227360, -
2.61e-49FFCP PHASE2:Hg19::chr7:27219754..27219759,-#_8d7f56b32c4ceb978dc8e0cd25b389f1p16@HOXA10
2.61e-49FFCP PHASE1:Hg19::chr7:27219754..27219759,-#_8d7f56b32c4ceb978dc8e0cd25b389f1p16@HOXA10
3.13e-49FFCP PHASE1:Hg19::chr21:41029235..41029269,+#_cb6a7b55cca1880a4f7ad4933a65e6c4p2@B3GALT5
3.13e-49FFCP PHASE2:Hg19::chr21:41029235..41029269,+#_cb6a7b55cca1880a4f7ad4933a65e6c4p2@B3GALT5
4.07e-49FFCP PHASE2:Hg19::chr9:133986782..133986794,+#_7b425cd6db298644c516d9f8cce7a9ddp4@AIF1L
4.07e-49FFCP PHASE1:Hg19::chr9:133986782..133986794,+#_7b425cd6db298644c516d9f8cce7a9ddp4@AIF1L
1.12e-47FFCP PHASE1:Hg19::chr7:140227303..140227330,-#_ef82af357830d3fe18fd0cf46689181dp@chr7:140227303..140227330, -
1.12e-47FFCP PHASE2:Hg19::chr7:140227303..140227330,-#_ef82af357830d3fe18fd0cf46689181dp@chr7:140227303..140227330, -
1.23e-44FFCP PHASE1:Hg19::chr20:6034576..6034592,-#_19bd1805b38afe06a5fdead62c331549p3@LRRN4
1.23e-44FFCP PHASE2:Hg19::chr20:6034576..6034592,-#_19bd1805b38afe06a5fdead62c331549p3@LRRN4
3.62e-44FFCP PHASE2:Hg19::chr21:46826248..46826282,-#_f3c35e46584d337ee531019dd328eed7p@chr21:46826248..46826282, -
3.62e-44FFCP PHASE1:Hg19::chr21:46826248..46826282,-#_f3c35e46584d337ee531019dd328eed7p@chr21:46826248..46826282, -
3.06e-43FFCP PHASE2:Hg19::chr20:6034672..6034714,-#_05adfd5cadfc15a651c461e70aa3e8bdp2@LRRN4
3.06e-43FFCP PHASE1:Hg19::chr20:6034672..6034714,-#_05adfd5cadfc15a651c461e70aa3e8bdp2@LRRN4
1.81e-42FFCP PHASE1:Hg19::chr15:85403302..85403304,+#_954155af47effd887e015be19546209dp@chr15:85403302..85403304, +
1.81e-42FFCP PHASE2:Hg19::chr15:85403302..85403304,+#_954155af47effd887e015be19546209dp@chr15:85403302..85403304, +
1.82e-42FFCP PHASE1:Hg19::chr7:98453821..98453843,-#_f90e31b09ed039489065c2f0b3b8f880p@chr7:98453821..98453843, -
1.82e-42FFCP PHASE2:Hg19::chr7:98453821..98453843,-#_f90e31b09ed039489065c2f0b3b8f880p@chr7:98453821..98453843, -
2.77e-42FFCP PHASE1:Hg19::chr20:6034598..6034603,-#_64f0fb9488c34d7aa35fa7ddfc615754p7@LRRN4
2.77e-42FFCP PHASE2:Hg19::chr20:6034598..6034603,-#_64f0fb9488c34d7aa35fa7ddfc615754p7@LRRN4
7.5e-42FFCP PHASE2:Hg19::chr10:102505493..102505546,+#_f0d6608134f331212076b0cf8c4feb5ap2@PAX2
7.5e-42FFCP PHASE1:Hg19::chr10:102505493..102505546,+#_f0d6608134f331212076b0cf8c4feb5ap2@PAX2
3.59e-41FFCP PHASE1:Hg19::chr9:71735910..71735923,+#_38c36254e84751066bd0fb268449085cp16@TJP2
3.59e-41FFCP PHASE2:Hg19::chr9:71735910..71735923,+#_38c36254e84751066bd0fb268449085cp16@TJP2
9.39e-41FFCP PHASE1:Hg19::chr1:94713418..94713436,+#_da5774721cd42bc6dacef1458cf4e5acp1@ENST00000413103
9.39e-41FFCP PHASE2:Hg19::chr1:94713418..94713436,+#_da5774721cd42bc6dacef1458cf4e5acp1@ENST00000413103
1.7e-40FFCP PHASE1:Hg19::chr20:6034828..6034857,-#_7e64db74d0108c568a50396c061125d7p5@LRRN4
1.7e-40FFCP PHASE2:Hg19::chr20:6034828..6034857,-#_7e64db74d0108c568a50396c061125d7p5@LRRN4
2.9e-40FFCP PHASE1:Hg19::chr1:20465872..20465881,+#_0db73e57a738d395ccb58a014c9680d5p2@PLA2G2F
2.9e-40FFCP PHASE2:Hg19::chr1:20465872..20465881,+#_0db73e57a738d395ccb58a014c9680d5p2@PLA2G2F
8.58e-40FFCP PHASE1:Hg19::chr9:133986807..133986821,+#_7292c1f098e7106d98dd317e9b5a04f6p3@AIF1L
8.58e-40FFCP PHASE2:Hg19::chr9:133986807..133986821,+#_7292c1f098e7106d98dd317e9b5a04f6p3@AIF1L
1.21e-39FFCP PHASE2:Hg19::chr2:31361432..31361442,-#_66c269e46af0036702da9dd8c893c98cp6@GALNT14
1.21e-39FFCP PHASE1:Hg19::chr2:31361432..31361442,-#_66c269e46af0036702da9dd8c893c98cp6@GALNT14
3.08e-39FFCP PHASE1:Hg19::chr20:6033120..6033128,-#_2f85ef56c017252e7af908b3e5d50499p4@AB527789
3.08e-39FFCP PHASE2:Hg19::chr20:6033120..6033128,-#_2f85ef56c017252e7af908b3e5d50499p4@AB527789
7.42e-37FFCP PHASE1:Hg19::chr6:24358114..24358125,-#_53982ee8be35e583abe5fc74e6bdaf67p4@DCDC2
7.42e-37FFCP PHASE2:Hg19::chr6:24358114..24358125,-#_53982ee8be35e583abe5fc74e6bdaf67p4@DCDC2
1.29e-36FFCP PHASE2:Hg19::chr2:693362..693373,+#_29e9f7b8da42d639f074d35c43b0df77p@chr2:693362..693373, +
1.29e-36FFCP PHASE1:Hg19::chr2:693362..693373,+#_29e9f7b8da42d639f074d35c43b0df77p@chr2:693362..693373, +
1.36e-36FFCP PHASE1:Hg19::chr2:177016336..177016350,+#_3ecd9c5cffedfeed2f6570856eb3696ep1@HOXD4
1.36e-36FFCP PHASE2:Hg19::chr2:177016336..177016350,+#_3ecd9c5cffedfeed2f6570856eb3696ep1@HOXD4
6.21e-36FFCP PHASE1:Hg19::chr2:176982078..176982095,+#_21e5b7dca00acec5f668f050f557961bp@chr2:176982078..176982095, +
6.21e-36FFCP PHASE2:Hg19::chr2:176982078..176982095,+#_21e5b7dca00acec5f668f050f557961bp@chr2:176982078..176982095, +
2.64e-35FFCP PHASE2:Hg19::chr20:6033140..6033181,-#_887908662d234baad1731f1a0b414967p1@AB527789
2.64e-35FFCP PHASE1:Hg19::chr20:6033140..6033181,-#_887908662d234baad1731f1a0b414967p1@AB527789
3.85e-35FFCP PHASE1:Hg19::chr2:108994466..108994485,+#_28c49459b8535ab5a1b9b2508fc5af81p3@SULT1C4
3.85e-35FFCP PHASE2:Hg19::chr2:108994466..108994485,+#_28c49459b8535ab5a1b9b2508fc5af81p3@SULT1C4
8.14e-35FFCP PHASE1:Hg19::chr18:43405633..43405645,+#_80f51aaf68a29d4c7f52f80429207d00p4@SIGLEC15
8.14e-35FFCP PHASE2:Hg19::chr18:43405633..43405645,+#_80f51aaf68a29d4c7f52f80429207d00p4@SIGLEC15
1.65e-34FFCP PHASE2:Hg19::chr10:91043420..91043437,+#_923d5fb94736621af1adbe7cf12ccbb7p1@ENST00000444849
1.65e-34FFCP PHASE1:Hg19::chr10:91043420..91043437,+#_923d5fb94736621af1adbe7cf12ccbb7p1@ENST00000444849
1.14e-33FFCP PHASE1:Hg19::chr17:171147..171161,+#_7d09be66a658d9a3d2a78c916befd87cp@chr17:171147..171161, +
1.14e-33FFCP PHASE2:Hg19::chr17:171147..171161,+#_7d09be66a658d9a3d2a78c916befd87cp@chr17:171147..171161, +
1.52e-33FFCP PHASE1:Hg19::chr14:57960456..57960478,-#_36ef14889442b1969fd90bfe7c17db2ap2@C14orf105
1.52e-33FFCP PHASE2:Hg19::chr14:57960456..57960478,-#_36ef14889442b1969fd90bfe7c17db2ap2@C14orf105
1.8e-33FFCP PHASE1:Hg19::chr2:31361543..31361564,-#_f966a962ed51eba4bb4a8ef49057170ap5@GALNT14
1.8e-33FFCP PHASE2:Hg19::chr2:31361543..31361564,-#_f966a962ed51eba4bb4a8ef49057170ap5@GALNT14
2.35e-33FFCP PHASE1:Hg19::chr3:190105935..190105966,+#_1b7e7fc17aa55023f5fa6806c9e1aa1ep1@CLDN16
2.35e-33FFCP PHASE2:Hg19::chr3:190105935..190105966,+#_1b7e7fc17aa55023f5fa6806c9e1aa1ep1@CLDN16
4.12e-33FFCP PHASE1:Hg19::chr17:36065029..36065045,-#_d8fd521c9f9c47fbc7b6e915725c475ep@chr17:36065029..36065045, -
4.12e-33FFCP PHASE2:Hg19::chr17:36065029..36065045,-#_d8fd521c9f9c47fbc7b6e915725c475ep@chr17:36065029..36065045, -
8.12e-33FFCP PHASE2:Hg19::chr17:35293950..35293973,-#_11073641f9129332db4ff65d5684971ep1@ENST00000528383, p1@ENST00000529264, p1@ENST00000532387
8.12e-33FFCP PHASE1:Hg19::chr17:35293950..35293973,-#_11073641f9129332db4ff65d5684971ep1@ENST00000528383, p1@ENST00000529264, p1@ENST00000532387
1.25e-32FFCP PHASE1:Hg19::chr22:30653574..30653606,-#_1eb70767d03fe355a5e1309b70987709p@chr22:30653574..30653606, -
1.25e-32FFCP PHASE2:Hg19::chr22:30653574..30653606,-#_1eb70767d03fe355a5e1309b70987709p@chr22:30653574..30653606, -

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=UBERON:0004208&oldid=3277640"