Question: how to calculaute Tissue Specificity of genes
0
gravatar for Bioiris
2.0 years ago by
Bioiris0
Bioiris0 wrote:

salut,

I have a count table , and I need to calculate the tissue specificity of genes

table(A) ————————

gene_id sample1 sample2 sample3 . ……..sample20 g1 23 0 1 3 g2 35 1 4 8 g3 4 6 70 0 g4 98 12 7 6 g5 60 2 8 12 . . . g1907 13 0 0 0

is there a tool that calculates tissue specificity ??

Thanks.

rna-seq • 613 views
ADD COMMENTlink modified 2.0 years ago by Charles Plessy2.5k • written 2.0 years ago by Bioiris0
1

There are multiple methods to estimate tissue specificity. Here's an article that compares some approaches: http://bib.oxfordjournals.org/content/early/2016/02/17/bib.bbw008.full

ADD REPLYlink written 2.0 years ago by spvensko180

I am doing the same thing. I read that paper last night. Very fast read ...recommends the TAU method. But also points to some pitfalls to avoid.

Other papers from this year:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4932457/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4968975/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4916594/

What tissue are you working on?

ADD REPLYlink modified 2.0 years ago • written 2.0 years ago by YaGalbi1.3k

Try Jaccard index, I have used them with RNAseq data before.

ADD REPLYlink written 2.0 years ago by Hranjeev1.4k
0
gravatar for Satyajeet Khare
2.0 years ago by
Satyajeet Khare1.3k
Pune, India
Satyajeet Khare1.3k wrote:

You can use Specificity matrix in cummeRbund. S=1 if the gene is expressed exclusively in that sample.

ADD COMMENTlink written 2.0 years ago by Satyajeet Khare1.3k
0
gravatar for Charles Plessy
2.0 years ago by
Charles Plessy2.5k
Japan
Charles Plessy2.5k wrote:

I like the richness index that is implemented in the "rarefy" function of the "vegan" package for R. For example, if one calculates the richness index on a scale (subsample size) of 10 for a given gene, it is basically asking the question of how many samples would seen be expessing that gene if the total number of counts for that gene were 10. The lower the richness, the higher the tissue specificity. To normalise the expression table before calculating the richness, I downsample all the libraries at the same level. Note as well that a meaningful richness index can not be calculated on a scale that is lower than the total number of counts for a given gene. Thus, in the example above, genes with less than 10 counts in total over all the sample should be excluded.

ADD COMMENTlink written 2.0 years ago by Charles Plessy2.5k
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