Question: gene expression correlation positive controls scRNAseq
0
gravatar for guillaume.rbt
3 months ago by
guillaume.rbt800
France
guillaume.rbt800 wrote:

Hi all,

I'm currently testing tools to assess the correlation of gene expression with scRNAseq human data.

I would like to have housekeeping "positive controls" of two genes that are always highly correlated, in any type of cell.

Would anyone know an example of a pair of gene like this?

Thanks

ADD COMMENTlink modified 3 months ago by geek_y11k • written 3 months ago by guillaume.rbt800
1

One potential resource: https://www.tau.ac.il/~elieis/HKG/

Of course, with the dropouts in scRNA-seq, it's going to be difficult to get any meaningful correlations.

ADD REPLYlink modified 3 months ago • written 3 months ago by igor11k

thanks ! I've found ABCF1 and ABCF2 that seems to be good candidates (R=0.81 on all TCGA normal samples)

ADD REPLYlink written 3 months ago by guillaume.rbt800

TCGA is not single-cell. Did you mean "RNAseq" instead of "scRNAseq" in the title?

ADD REPLYlink written 3 months ago by igor11k

I used TCGA to check quickly the correlation between the genes, but I indeed work on scRNAseq.

ADD REPLYlink written 3 months ago by guillaume.rbt800
1
gravatar for geek_y
3 months ago by
geek_y11k
Barcelona
geek_y11k wrote:

In this paper, Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data, Nat Methods, authors did generate loads of simulated data sets as ground truth. Their method allows to plugin any algorithms and let you asses your method.

You can access to their synthetic data and code on GitHub .

BTW, its already a benchmarking paper. Might save time for you in testing methods.

ADD COMMENTlink modified 3 months ago • written 3 months ago by geek_y11k
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