RefG Heart Development co-curation (Archived)

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Title of Project: Heart Development co-curation

Lead group, lead curator

BHF-UCL group, Varsha Khodiyar; Cardiovascular GO annotation initiative

Reference Genome Start Date Preference

April 2010

Number of proposed targets

60

Short description to background of proposed project

The recent ontology workshop on heart development terms means that the ontology to support the annotation of this set of genes already exists.


The heart is interesting from an evolutionary standpoint, for example fish have a 4-chambered heart, with the chambers arranged in a sequential manner, and frogs have a 3-chambered heart. Therefore it will be interesting to see how the functions of the gene products change across species.


The heart is also of interest from the viewpoint of human health. There are many model organisms used to study the heart and this project will help to annotate the gene products of organisms that are important to cardiovascular research, but are not reference genome species, for example the dog.


The target list is rich in proteins involved in a number of central signaling pathways, TGF-beta and Wnt-catenin signaling for example. Thus, the annotation of this set will also serve as a through test and aid ongoing improvements of the new signaling ontology.

Description of target selection

During the heart development workshop, the heart experts were asked for their opinions as to which genes were important in specific developmental processes. This list was combined with literature reviews to generate further genes of interest. This set was sent back to the heart experts for review and 4 of their additional suggestions were incorporated. Additionally, 18 targets have been included for which the only evidence gathered is that the mouse ortholog has been annotated with one (or more) of the following mammalian phenotype terms:

  • MP:0003974 - abnormal endocardium morphology
  • MP:0008825 - abnormal cardiac epithelial to mesenchymal transition
  • MP:0004252 - abnormal direction of looping morphogenesis

It expected that as annotation proceeds, the literature will further support the inclusion of these targets in the heart development set.

There are a number of other mammalian phenotype terms which are relevant to heart development, but which have not been selected in this target set. The reason is that the aim was to generate a list of only 60 panther families. However, as the annotation proceeds it is likely that additional targets will become obvious, the annotation of which would help the heart development annotation set to feel more complete. So if possible, it is suggested that the option of adding an extra month to the project would be beneficial. This would allow time for the annotation of new targets that have come out of the initial 3-month project.


Previous reference genome targets

The initial heart development set from the experts included 24 previous reference genome targets. Of these, seven were ref genome targets prior to May 09 and so it is felt that they will benefit from further annotation with the updated ontology. The remaining 17 were in the mouse lung target set. Of these only 3 of the human genes are fully annotated at the time of writing. The remaining 14 require annotation both for the mouse lung project and the heart development project. It is suggested these 14 targets are given the highest possible priority, as they are important for both the mouse lung project and heart development. However, as they had been selected previously they are not included in the set of 60 heart development targets.


Limitations of target set

The Panther subfamily has been specified where possible in order to minimize the number of non-heart development related proteins included in each family. Where there are multiple targets within a panther group, the family member specifically shown to be involved in heart development will be highlighted on the wiki as a higher priority than other non-heart development related family members. Many of the proposed targets may not be represented by orthologues in non-chordate species. Therefore an alternative set of targets may need to be found for Reference Genome groups annotating to non-chordate species.


Reference Genome Annotation Plans

A central document page will be developed and be accessible by all concerned. This page will act as a central resource for the project and will help in monitoring progress, highlight interesting points/difficulties, supported by email communication between all the curators involved. The page should also capture any data that could be considered for publication purposes.


Ideas for annotation data exploitation

The annotations will be analyzed at the end of the project, to see if GO annotations can highlight the functional differences between species. Ongoing contact with heart development experts will be maintained to seek additional value for the project.


Heart Development Review Papers

  1. PMID: 19647421 Protein interactions at the heart of cardiac chamber formation

Review of the heart across species.

  1. PMID: 19592411 'And the beat goes on.' The cardiac conduction system: the wiring system of the heart.

Review of cardiac conduction system development

  1. PMID: 19390062 Signaling pathways controlling second heart field development

Review of signaling in second heart field development

  1. PMID: 19371733 Shaping the zebrafish heart: from left-right axis specification to epithelial tissue morphogenesis

Review of zebrafish heart development

  1. PMID: 17098821 Another key role for the cardiac neural crest in heart development

Neural crest cell contribution to heart development

  1. PMID: 20186050 The molecular genetics of congenital heart disease: a review of recent developments

Review of transcription factors involved in heart development

  1. PMID: 20201901 Developmental basis of adult cardiovascular diseases

EMT contribution to heart valve development


Annotation Targets

Panther Family Gene Symbol Heart Development stage General process Support for Role in heart development (Human protein ID)

  1. PTHR10568:SF4 DKK1 (O94907) Specification of cardiac precursor cells Wnt/beta-catenin pathway PMID: 18297060
  2. PTHR20937:SF2 MESP1 Specification of cardiac precursor cells Wnt/beta-catenin pathway PMID: 18297060
  3. (Q9BRJ9) PMID: 11369261
  4. MP:0008825
  5. MESP2 PMID: 10887078
  6. (Q0VG99)
  7. PTHR24204:SF26 ISL1 (P61371) Specification of cardiac precursor cells PMID: 19571884
  8. PMID: 17519333
  9. PTHR11267:SF15 T (O15178); brachyury Specification of cardiac precursor cells Transcription factor PMID: 18767184
  10. PTHR22793:SF4 MYOCD (Q8IZQ8) Specification of cardiac muscle cells regulation of smooth muscle gene expression PMID: 15907818
  11. Pete Scambler
  12. PTHR11945:SF24 MEF2A (Q02078) Cardiac muscle cell specification Transcription factor PMID: 19161138
  13. PTHR11945:SF46 PMID: 16043483
  14. PMID: 10458488
  15. PMID: 11316766
  16. PMID: 16469744
  17. PTHR18973:SF26 ISL1 (P61371) Expressed by cardiac progenitor cells Beta-catenin signaling PMID: 17519333
  18. Hedgehog-smoothened signaling
  19. PTHR23349:SF3 HAND1 (O96004); eHAND Cardiac muscle cell specification Transcription factor PMID: 12909338
  20. Ventricular morphogenesis PMID: 19586923
  21. PMID: 18276607
  22. PTHR12198:SF0 PROX1 (Q92786) Cardiomyocyte morphogenesis Transcription factor PMID:19091769
  23. PTHR11945:SF25 MEF2C (Q06413) Myocardium development Transcription factor PMID: 16469744
  24. PMID: 19899118
  25. PTHR22824:SF3 AKAP13 (Q12802) Myocardium development Kinase signaling PMID: 20139090
  26. PTHR11878:SF6 SLC8A1 (P32418) Sodium ion transport MP:0003974
  27. PTHR13703:SF20 SMAD6 (O43541) TGF-beta signaling MP:0003974
  28. PTHR10032:SF32 OVOL2 (Q9BRP0) Seems to have a role in development in general, but is on BHF list Transcription factor MP:0003974
  29. Notch signaling
  30. PTHR23341:SF2 HMGA2 (P52926) Cardiomyocyte differentiation Regulation of NKX2.5 transcription PMID: 18425117
  31. PTHR12027:SF7 WNT11 (O96014) Cardiovascular progenitor cells Beta-catenin signaling PMID: 17519333
  32. PTHR23349:SF2 HAND2 (P61296); dHAND Outflow tract development Transcription factor PMID: 12909338
  33. PTHR23349:SF19 Cardiac muscle cell differentiation PMID: 20144608
  34. PMID: 19607825
  35. PTHR11036:SF11 SEMA6D (Q8NFY4) Cardiac cell migration semaphorin-plexin signaling pathway PMID: 14977921
  36. PTHR22625:SF13 PLXNA1 (Q9UIW2) Cardiac cell migration semaphorin-plexin signaling pathway PMID: 14977921
  37. PTHR19134:SF64 PTPN11 (Q06124) MP:0008825
  38. No panther family? C2CD3 (Q4AC94) MP:0004252
  39. PTHR14949:SF1 CFC1 (Q9GZR3) MP:0004252
  40. PTHR10494:SF2 NOG (Q13253); Noggin BMP inhibition MP:0004252
  41. PTHR11339:SF39 CHRD (Q9H2X0) MP:0004252
  42. PTHR16186:SF1 DAND5 (Q8N907) MP:0004252
  43. PTHR10676:SF17 DYNC2H1 (Q8NCM8) MP:0004252
  44. PTHR13236 DYNC2LI1 (Q8TCX1) MP:0004252
  45. PTHR10795:SF3 FURIN (P09958) MP:0004252
  46. PTHR10878:SF8 DVL2 (O14641) MP:0004252
  47. PTHR19264:SF69 EDNRB (P24530) MP:0004252
  48. PTHR11984:SF5 GJC1 (P36383) MP:0004252
  49. PTHR11304:SF18 EFNB2 (P52799) MP:0003974
  50. MP:0004252
  51. PTHR13831 HIRA (P54198) MP:0004252
  52. PTHR15722:SF2 IFT172 (Q9UG01) MP:0004252
  53. PTHR14066:SF2 NPPA (P01160); ANF Heart chamber marker natriuretic peptide family PMID: 16002056
  54. PTHR14066:SF3 PMID: 2522772
  55. PMID: 2147704
  56. PTHR10812:SF8 TFAP2 (P05549) Heart morphogenesis Transcription factor PMID: 12586840
  57. PMID: 18275040
  58. PMID: 14975722
  59. PTHR11267:SF26 TBX20 (Q9UMR3) Heart morphogenesis Transcription factor PMID: 18275040
  60. PMID: 18834961
  61. PMID: 17668378
  62. Pete Scambler
  63. PTHR11389:SF375 SNAI2 (O43623) Cardiac cushion morphogenesis Epithelial-to-mesenchymal transition (EMT) PMID: 18663143
  64. SNAI1 (O95863)
  65. PTHR23349:SF6 TWIST1 (Q15672) Cardiac neural crest morphogenesis Epithelial-to-mesenchymal transition (EMT) PMID: 18539270
  66. PTHR11848:SF58 NODAL (Q96S42) Left/right patterning BMP signaling PMID: 19064609
  67. PTHR17045:SF2 CITED2 (Q99967) Left/right patterning Heart morphogenesis, specifically cardiac septal defects PMID: 16287139
  68. PMID: 15750185
  69. MP:0004252
  70. PTHR24329:SF179 PITX2 (Q99697) Left/right patterning Wnt/beta-catenin pathway PMID: 12732450
  71. PMID: 12464179
  72. PTHR11309:SF35 SMO (Q99835) Left/right patterning Hedgehog-smoothened signaling PMID: 19654211
  73. PMID: 16687132
  74. PMID: 11517919
  75. PTHR11889:SF17 IHH (Q14623) Left/right patterning Hedgehog-smoothened signaling PMID: 11517919
  76. PTHR11201:SF220 DLL1 (O00548) Left/right patterning Regulation of transcription, Notch signaling PMID: 12441287
  77. MP:0004252
  78. PTHR11829:SF1 FOXA2 (Q9Y261); HNF-3 beta Possible roles in left/right patterning and heart looping Regulation of transcription PMID: 9466889
  79. PMID: 12062060
  80. MP:0004252
  81. PTHR12958 ZFPM1 (Q8IX07); FOG1 Heart looping Transcription factor? PMID: 16316643
  82. PMID: 14614148
  83. PTHR11945:SF32 SRF (P11831); serum response factor Angiogenesis Transcription factor PMID: 17629633
  84. Heart looping PMID: 15492011
  85. Pete Scambler
  86. PTHR10799:SF70 CHD7 (Q9P2D1) Seems to have a role in development in general, but is on BHF list. DNA helicase? PMID: 15300250
  87. PMID: 17661815
  88. Pete Scambler
  89. PTHR12881:SF2 MED1 (Q15648) Seems to have a role in development in general, but is on BHF list Brings transcription factor (GATA1) and RNA pol II together PMID: 11724781
  90. PMID: 17132730
  91. PTHR10373:SF11 LEF1 (Q9UJU2) Cannot find evidence of heart development role. But is on BHF list and came up in PMID:18593560 microarray analysis Wnt signalling, transcription factor PMID: 18579517
  92. PTHR24338:SF137 MSX1 (P28360) Atrioventricular myocardium and AV valve formation BMP signaling, Notch signaling PMID: 18667074
  93. MSX2 (P35548)
  94. PTHR10985:SF9 HEY2 (Q9UBP5); HESR2 Ventricular septation, blood vessel development Notch signaling PMID: 16329098
  95. PMID: 16165016
  96. PTHR24247:SF85 HTR2B (P41595) Heart trabeculation ErbB-2 receptor signaling PMID: 15075741
  97. Possible role in heart valve development PMID: 11728882
  98. PMID: 18511249
  99. PTHR24044:SF219 NOTCH1 (P46531) Outflow tract development Notch signaling PMID: 17967789
  100. PTHR24838:SF73 Left ventricle development Epithelial-to-mesenchymal transition (EMT) PMID: 18593716
  101. PTHR12365 SPRY1 (O43609) Outflow tract development FGF signaling PMID: 18832392
  102. ERK cascade PMID: 15306693
  103. PTHR23043:SF7 HIF1A (Q16665) Angiogenesis Regulation of NKX2-5 PMID: 18303027
  104. Epithelial-to-mesenchymal transition (EMT) PMID: 19491109
  105. MP:0004252
  106. PTHR13844 SMARCD3 (Q6STE5); Baf60c Cardiac myocyte differentiation Notch signaling PMID: 19396158
  107. Left/right patterning PMID: 17210915
  108. PMID: 15525990
  109. Pete Scambler
  110. PTHR18958:SF179 ANKRD1 (Q15327) myofibrillar stretch-sensor system Regulation of transcription PMID: 19525294
  111. PMID: 19299913
  112. PMID: 18956313
  113. PTHR11267:SF20 TBX18 (O95935) Cardiac conduction system development Transcription factor PMID: 19213963