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I have a file like this with 2 columns. I want to separate the columns based on plus and minus signs into separate files. How do I do this with awk or sed. Kindly help.

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What do you want to do with NA values?

The below scripts ignore them (h3ab74's answer will print them to positiveExpression)

awk '$2 ~ /^[0-9]+$/  {print $0}' expressionFile.txt > positiveExpression.txt
awk '$2 ~ /^-[0-9]+$/ {print $0}' expressionFile.txt > negativeExpression.txt

These do a regex match to respectively, positive and negative numbers. If there's anything else in field 2 the line won't be printed.

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awk '{if($2>0) print $0}' expressionFile.txt >> positiveExpression.txt
awk '{if($2<0) print $0}' expressionFile.txt >> negativeExpression.txt

Assuming that the file with gene expressions has the title: expressionFile.txt, this should do the trick.

Explanation of first line of code: if values in the 2nd column - $2 - are greater than 0, print all columns ($0) and write to a file (>>) titled, positiveExpression.txt. The use of awk '{}' is just syntactical.

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