Terms in COXPRESdb

last update; May. 30. 2022

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Terms in COXPRESdb

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Coexpression z score

Most gene pairs show random-level coexpression scores, which are normally distributed. Therefore, we adopted a coexpression z-score, where 0 is a random level, and 3 is a false positive rate of 0.1% for any species or version. Some gene pairs show larger coexpressions than the normal distribution of the random coexpression. The deviation is apparent around z>3, suggesting that coexpression with z>3 is a useful when using COXPRESdb.

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]

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
Function

The annotation file ("gene_info") released by NCBI is used in COXPRESdb.

MR^*	Edge
MR < 5	Bold edge
MR < 30	Normal edge
MR > 30	Thin edge

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]

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

KEGG (Kyoto Encyclopedia of Genes and Genemes) was developed by Genomenet. Annotation of bioche\ mical pathways were used in COXPRESdb.
Logit Score (LS)
Logit Score between a pair of genes is calculated as follows,
- p = MR / N
- logit(p) = log2(p / (1-p))
- LS = - logit(p)
- N: Number of genes in the platform.
About logit function in coexpression calculation, please also check our paper.
Obayashi et al. (2018) ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index.

z score of LS Edge

z > 7 Bold edge

z > 5 Normal edge

z ≤ 5 Thin edge
NCBI Gene Info.

Annotation released by NCBI Gene.
Tax ID
The following species uses multiple taxonomy IDs for different purposes.
- Sce:
- ncbi gene: 4932, 559292
- RNAseq coexpression
- SRA retrieval: 4932, 559292
- SRA mapping (refseq): 559292

z score of LS	Edge
z > 7	Bold edge
z > 5	Normal edge
z ≤ 5	Thin edge

Tissue specific expression pattern

Localization name

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.

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.