Agenda for Kidney Content Meeting

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Please suggest agenda items, relevant papers and other information relating to kidney development GO terms that you would like discussed at this workshop, to enable us to form an agenda.


GO annotators GO Editors Kidney Development Experts
Dr Yasmin Alam-Faruque (GOA)
Dr Emily Dimmer (GOA)
Dr Rebecca Foulger (UniProt/Xenopus)
Dr Susan Tweedie (Flybase)
Dr Rachael Huntley (GOA)
Dr Midori Harris
Dr David Hill
Professor Adrian Woolf
Professor Jamie Davies
Dr Duncan Davidson


EMBL-EBI, Room C202/203 - shared facilities, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD. Date: Monday 25th January 2010, 9:30am to 5pm


9:15am Tea/ Coffee and biscuits
9:30am Welcome and introduction Yasmin
9:35am Introduction to GO David Hill
9:45am Kidney precursor cells and tissues (segmentation)
* Development of kidney field
* Nephrogenic stem cell differentiation.
* Sensing a quorum of cells / control of the number of cells in a cell group
* (Mesonephric/metanephric) mesenchyme-epithelial transition
* Epithelial patterning of the nephron epithelium
* proximal/distal nephron tubule patterning/ specification/ identity;
* Formation of tight junctions/ adherens junctions/ basement membrane,
* specification of distal tubule identity; pronephros proximal/distal patterning and development
*SF -SF 2859892: specification of kidney anlage *PMID 18715948
* SF -SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
11am Coffee break
11:20am Kidney morphogenesis - Kidney structure formation
*Cell morphogenesis
*Formation of renal vesicle,
*Formation of comma-shaped body/ S-shaped body/ glomerulus
*Formation of mesangium,
* Oriented mitosis
* new children of GO:0002070 epithelial cell maturation: Podocyte/ Proximal tubule/ Loop of Henle/ Distal tubule/ Connecting tubule cell differentiation (and other nephron cell types)
* SF -SF 2903833: kidney glomus development *PMID 10572058
* SF -SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
12:30pm Lunch
1:30pm Anatomical structure development/ Formation
*Macula densa development
* Regulation of epithelial tubule diameter (is_a GO:0035296 regulation of tube diameter)
* Morphogenesis of epithelial tubules
*mesonephric tubule (anterior and posterior in mouse)
*nephric duct/ tubule specification/differentiation/morphogenesis
*Collecting duct system development/formation/differentiation
*Connecting tubule development
*kidney proximal tubule development;
* SF -SF 2902547: various kidney development terms *PMID 16790474 *PMID 18835385
* SF -SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
* SF -SF 2903833: kidney glomus development *PMID 10572058
3pm Coffee break
3:20pm Continue with Anatomical structure development/ Formation
* Connection of nephron tubule to collecting duct
* proximal convoluted tubule development/ specification;
*kidney intermediate tubule development/ identity specification:- thin descending limb development; thin ascending limb development; thick ascending limb development;
*kidney distal tubule development:- distal convoluted tubule development/ specification
*Signalling to blood vessel-forming cells (GO:0060684 epithelial-mesenchymal cell signaling?)
*renal smooth muscle cell differentiation
* SF -SF 2902547: various kidney development terms *PMID 16790474 *PMID 18835385
* SF -SF 2860000: proximodistal kidney segmentation *PMID 17875669 *PMID 18715948 *PMID 12925600
* SF -SF 2903833: kidney glomus development *PMID 10572058
5pm Close


Current Kidney Development Ontology Terms

The currently available kidney development process ontology (November 2009) [[1]]
*GO:0001656 GO:0001657 GO:0001658 GO:0001822 GO:0001823 GO:0032835 GO:0032836 GO:0034671 GO:0034672 GO:0048793 GO:0060675 GO:0060676 GO:0060677 GO:0060678 GO:0060679 GO:0060680 GO:0060681 GO:0060682

Relevant papers and other resources

  • Kidney Development Review Papers:
  • PMID 15554941 Transcriptional control of kidney development. Bouchard M. 2004. Talks about genes involved in nephric lineage specification (Pax2/Pax8/Lim1/Bmp4/Wt1/GDNF1/Eya1/Foxc1); metanephros development - UB positioning, induction, nephron induction, ureter branching, Stromal cell differentiation(Gdnf1/Eya1/Foxc1/2/Slit2/Robo2/Bmp4/Pax2/Hox11(HoxA11/C11/D11)/ Sall1/Wt1/Six1/Wnt4/Emx2/Gata3/BF2/Pod1/Pbx21.
  • PMID 15380247 Recent genetic studies of mouse kidney development. Yu J, McMahon AP, Valerius MT. 2004. Has a nice diagram of the stages of nephron formation on p.551. Also lists genes investigated with particular molecular regulation of outgrowth of the uteric bud and regulation of tubulogenesis (Table 1; p552 - Gdf1, Six1, Slit2/Robo2, Wnt1, Fras1+Grip1, Pod1, Pbx1, Brn1, Psen1/2).
  • PMID 16760375 Role of transcriptional networks in coordinating early events during kidney development. Boyle S, de Caestecker Mark. 2006. Has nice diagrams of stages of early mammalian kidney development. Reviews transcription factors in mesenephric mesenchyme: Eya1/ Foxc1/2/ Hoxa/c/d11/ Pax2/ Pbx1/ Rar-alpha/beta2/ Sall1/ Six1/ Wt1.
  • PMID 12094231 Coordinating early kidney development: lessons from gene targeting. Vainio S, Lin Y. 2002. Nice diagrams of kidney development. List of genes essential for early kidney development (Transcription Factors: Emx2/Eya1/Foxc1/Foxd1/Pax2/Rara,Rarb/Sall1/Wt1; Growth factors: Bmp4/Bmp7/Fgf7/Gdnf/Wnt4; Growth factors/receptors: Gfra1/Notch2/Ret; Proteoglycans and their biosynthetic enzymes: Hs2st/Gpc3.
  • Kidney Development Websites:
  • Mouse Anatomy Browser - [3]
  • FMA human anatomy browser- [4]
  • GUDMAP browser - [5]; Metanephros [6]; renal vesicle [7]

Other reviews