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Question: gene expression correlation positive controls scRNAseq
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gravatar for guillaume.rbt
3 months ago by
guillaume.rbt • 800
France
guillaume.rbt • 800 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
gene expression correlation scrnaseq • 139 views
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modified 3 months ago by geek_y ♦ 11k • written 3 months ago by guillaume.rbt • 800
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 REPLY • link modified 3 months ago • written 3 months ago by igor ♦ 11k

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

ADD REPLY • link written 3 months ago by guillaume.rbt • 800

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

ADD REPLY • link written 3 months ago by igor ♦ 11k

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

ADD REPLY • link written 3 months ago by guillaume.rbt • 800
1
gravatar for geek_y
3 months ago by
geek_y ♦ 11k
Barcelona
geek_y ♦ 11k 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 COMMENT • link modified 3 months ago • written 3 months ago by geek_y ♦ 11k
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