Data and databases Lars Juhl Jensen EMBL Heidelberg
a lot of data
 
a lot of databases
Duncan Hull, nodalpoint.org
genes and proteins
GenBank
 
 
UniProt
 
 
PDB
 
 
genomes
SGD Saccharomyces Genome Database
 
 
TAIR The Arabidopsis Information Resource
 
 
GeneDB
 
 
Ensembl
 
 
 
and many others
homology
orthology and paralogy
 
InParanoid
model organism databases
 
 
 
HomoloGene
Entrez
 
 
COG Clusters of Orthologous Groups
deep orthology
functional classes
 
OrthoMCL
high resolution
 
 
 
YOGY
meta-database
 
 
eggNOG
multiple resolutions
 
 
 
 
TreeFam
phylogenetic trees
 
 
 
protein domains
CDD Conserved Domain Database
NCBI BLAST
 
 
Pfam
high coverage
 
 
 
SMART
signal transduction
 
 
InterPro
meta-database
 
 
 
structural classification
SCOP
manual assignments
 
CATH
automatic assignments
 
cell cycle
evolution of expression
 
gene expression
microarrays
 
dynamics
GEO Gene Expression Omnibus
 
 
ArrayExpress
 
 
cell cycle
 
 
Cyclebase.org
 
 
 
SCEPTRANS
 
 
interactions
affinity purification
 
yeast two-hybrid
 
synthetic lethality
 
repositories
BioGRID
 
 
DIP Database of Interacting Proteins
 
 
 
IntAct
 
 
MINT Molecular Interactions Database
 
 
 
cell cycle
dynamic network
 
linear motifs
less than 10 residues
 
Prosite
 
ELM
 
Domino
 
 
PepCyber P~Pep
 
 
 
Phospho.ELM
 
 
PhosphoSite
 
 
PhosPhAt
 
 
 
Phosida
 
 
cell cycle
evolution of phosphorylation
 
complexes
CORUM
 
 
Gene Ontology
 
 
cell cycle
regulation of assembly
 
pathways
KEGG
broad coverage
 
 
iPath
 
 
EcoCyc
MetaCyc
metabolism
 
 
Reactome
elegant data model
 
PID Pathway Interaction Database
meta-database
 
 
models
BioModels
 
 
cell cycle
Cyclonet
 
 
 
 
CCDB
 
 
 
 
integration
STRING
 
benchmarking
 
transfer by orthology
 
 
Bayesian framework
 
signaling networks
NetworKIN
 
 
 
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Computational approaches to cell cycle analysis: Data and databases

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PhD Program in Computational Biology, Instituto Gulbenkian de Ciencia, Oeiras, Portugal, April 29-May 2, 2008

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Computational approaches to cell cycle analysis: Data and databases

  1. 1. Data and databases Lars Juhl Jensen EMBL Heidelberg
  2. 2. a lot of data
  3. 4. a lot of databases
  4. 5. Duncan Hull, nodalpoint.org
  5. 6. genes and proteins
  6. 7. GenBank
  7. 10. UniProt
  8. 13. PDB
  9. 16. genomes
  10. 17. SGD Saccharomyces Genome Database
  11. 20. TAIR The Arabidopsis Information Resource
  12. 23. GeneDB
  13. 26. Ensembl
  14. 30. and many others
  15. 31. homology
  16. 32. orthology and paralogy
  17. 34. InParanoid
  18. 35. model organism databases
  19. 39. HomoloGene
  20. 40. Entrez
  21. 43. COG Clusters of Orthologous Groups
  22. 44. deep orthology
  23. 45. functional classes
  24. 47. OrthoMCL
  25. 48. high resolution
  26. 52. YOGY
  27. 53. meta-database
  28. 56. eggNOG
  29. 57. multiple resolutions
  30. 62. TreeFam
  31. 63. phylogenetic trees
  32. 67. protein domains
  33. 68. CDD Conserved Domain Database
  34. 69. NCBI BLAST
  35. 72. Pfam
  36. 73. high coverage
  37. 77. SMART
  38. 78. signal transduction
  39. 81. InterPro
  40. 82. meta-database
  41. 86. structural classification
  42. 87. SCOP
  43. 88. manual assignments
  44. 90. CATH
  45. 91. automatic assignments
  46. 93. cell cycle
  47. 94. evolution of expression
  48. 96. gene expression
  49. 97. microarrays
  50. 99. dynamics
  51. 100. GEO Gene Expression Omnibus
  52. 103. ArrayExpress
  53. 106. cell cycle
  54. 109. Cyclebase.org
  55. 113. SCEPTRANS
  56. 116. interactions
  57. 117. affinity purification
  58. 119. yeast two-hybrid
  59. 121. synthetic lethality
  60. 123. repositories
  61. 124. BioGRID
  62. 127. DIP Database of Interacting Proteins
  63. 131. IntAct
  64. 134. MINT Molecular Interactions Database
  65. 138. cell cycle
  66. 139. dynamic network
  67. 141. linear motifs
  68. 142. less than 10 residues
  69. 144. Prosite
  70. 146. ELM
  71. 148. Domino
  72. 151. PepCyber P~Pep
  73. 155. Phospho.ELM
  74. 158. PhosphoSite
  75. 161. PhosPhAt
  76. 165. Phosida
  77. 168. cell cycle
  78. 169. evolution of phosphorylation
  79. 171. complexes
  80. 172. CORUM
  81. 175. Gene Ontology
  82. 178. cell cycle
  83. 179. regulation of assembly
  84. 181. pathways
  85. 182. KEGG
  86. 183. broad coverage
  87. 186. iPath
  88. 189. EcoCyc
  89. 190. MetaCyc
  90. 191. metabolism
  91. 194. Reactome
  92. 195. elegant data model
  93. 197. PID Pathway Interaction Database
  94. 198. meta-database
  95. 201. models
  96. 202. BioModels
  97. 205. cell cycle
  98. 206. Cyclonet
  99. 211. CCDB
  100. 216. integration
  101. 217. STRING
  102. 219. benchmarking
  103. 221. transfer by orthology
  104. 224. Bayesian framework
  105. 226. signaling networks
  106. 227. NetworKIN

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