Set of genes correlate with your gene

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7.5 years ago

waqasnayab ▴ 250

Hi,

I am in this situation:

Find genes correlate with a given gene in gene expression heatmap(data analysis)

I have two genes of interest (with 0.72 correlation to each other). I would like to find set of genes or cluster of genes that are correlated with these two genes? Is there any way to have a heatmap of top 5 correlated genes to my two genes of interest?

I have input of like this:

Genes   MygeneinterestA MygeneinterestB
DDR1    0.0634830504    0.0054455272
GUCA1A  -0.0131271582   0.053572876
UBA7    -0.1101264403   -0.0797316737
PTPN21  -0.2523412388   -0.2177850957
EPHB3   -0.0640084764   0.0527953252
TRADD   -0.0499531048   0.1662949165
PLD1    -0.0599397513   -0.2011697957
FNTB    -0.2625271489   -0.3401681914
...........
...
..
.

Thanks,

Waqas.

RNA-Seq R next-gen correlation • 1.6k views

ADD COMMENT • link 7.5 years ago by waqasnayab ▴ 250

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What are the numbers in your table?

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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these are the correlation values calculated from the expression values. The table shown here is just the transpose one.

ADD REPLY • link 7.5 years ago by waqasnayab ▴ 250

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So you just need to select the 5 highest values in that table?

ADD REPLY • link 7.5 years ago by WouterDeCoster 47k

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if I do that, so these are those five genes that highly correlated with my gene of interest....,,,!!!????

ADD REPLY • link 7.5 years ago by waqasnayab ▴ 250

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You calculated correlation coefficients and then select the most correlated genes, no? Are you confused?