Terms in COXPRESdb

• ExSim
  Expression similarity (ExSim) is the degree of similarity of gene expression pattern. It is calculated as pearson's correlation coefficient between 2 genes.
  

  MR*	edge
  MR < 5	bold edge
  MR < 30	normal edge
  MR < 30	thin edge

  
  
• KEGG
  KEGG (Kyoto Encyclopedia of Genes and Genemes) was developed by Genomenet. Annotation of biochemical pathways were used in COXPRESdb.
  
  
• Gene Ontology (GO)
  Gene Ontology released by NCBI was used.
  Prefix of original IDs of GO were changed in COXPRESdb according to those type (BP, CC and MF).

  Prefix	Type
  BP	Biological Process
  CC	Cellular Component
  MF	Molecular Function

  Evidence code [www.geneontology.org];
  

  code	description
  IC	inferred by curator
  IDA	inferred from direct assay
  IEA	inferred from electronic annotation
  IEP	inferred from expression pattern
  IGI	inferred from genetic interation
  IMP	inferred from mutant phenotype
  IPI	inferred from physical interaction
  ISS	inferred from sequence or structural similarity
  NAS	non-traceable author statement
  ND	no biological data available
  TAS	traceable author statemen

  loose hierarchy of the codes;
  [TAS/IDA] > [IMP/IGI/IPI] > [ISS/IEP] > [NAS] > [IEA]
  
  
  

• WoLF PSORT
  Protein subcellur localizations are predicted using WoLF PSORT, which is developped by Dr. Paul Horton in Computational Biology Research Center, AIST, Japan.
  "kNN"-derived scores are normalized 0 (not reliable) to 10 (most reliable) in COXPRESdb.

  Localization name

  Abbr		name
  E	E.R.	E.R.
  G	golg	golgi body
  K	cysk	cytoskeletal
  L	lyso	lysosome
  M	mito	mitochondria
  N	nucl	nuclear
  P	plas	plasma membrane
  S	extr	extracellular
  V	vacu	vacuole
  X	pero	peroxisome
  Y	cyto	cytoplasm

  Localization names joining two abbreviated names with "_", such as "cyto_nucl", indicate dual localization.
  
  

• function
  The annotation file ("gene_info") released by NCBI is used in COXPRESdb.
  
  
• tissue specific expression pattern
  

  species	Accession (Link to NCBI GEO)	# of tissues	Averaged # of reprecation	Reference
  Human	GSE3526	65	5.4	Roth RB et al.(2006)
  Mouse	GSE1986	17	1.0

  After RMA normalization, data were averaged for each tissue. Expression values were base-2 logarithm.
  

  Graph in gene page

  Click to enlarge. Colors in tissue-specific expression graph in gene page indicate probesets corresponding to the gene.