VeryGene - Marker List for Human Tissues
Description
Marker gene list for Human tissues created from the
VeryGene dataset. Genes are ordered
according to their specificity index.
Source
Details
Note that according to the VeryGene paper, tissue
specific gene sets in this list are not
disjoint, and "express selectively in approximately two
tissues on average". This can be important when used in
deconvolution methods that require disjoint sets of
marker genes. Duplicates accross tissue types can be
removed using the function rmDuplicated or
by filtering on the specificity score, e.g., ml[ ml
>= 8].
Examples
vg <- MarkerList('VeryGene')
# marker sets are not disjoint
hasDuplicated(vg)
## [1] 32
# show historgram of specificity scores
hist(vg)
# filter on scores
vg2 <- vg[vg >= 8, drop=TRUE]
summary(vg2)
## Length Class Mode
## Adrenal gland 16 -none- numeric
## Bladder 1 -none- numeric
## Blood 134 -none- numeric
## Body of stomach 6 -none- numeric
## Bone marrow 1 -none- numeric
## Bone structure 3 -none- numeric
## Breast 2 -none- numeric
## Bronchus 1 -none- numeric
## Dura mater 5 -none- numeric
## Fallopian tube 1 -none- numeric
## Gallbladder 2 -none- numeric
## Hypothalamus 3 -none- numeric
## Larynx 1 -none- numeric
## Liver 129 -none- numeric
## Locus ceruleus 1 -none- numeric
## Lung 8 -none- numeric
## Medulla of kidney 1 -none- numeric
## Ovary 2 -none- numeric
## Pancreas 34 -none- numeric
## Placenta 26 -none- numeric
## Prostate 14 -none- numeric
## Pylorus 1 -none- numeric
## Right atrium 1 -none- numeric
## Salivary gland 3 -none- numeric
## Skin 7 -none- numeric
## Spleen 2 -none- numeric
## Substantia nigra 2 -none- numeric
## Testis 50 -none- numeric
## Thymus 33 -none- numeric
## Thyroid gland 8 -none- numeric
## Ureter 1 -none- numeric
## Vas deferens 3 -none- numeric