This pipeline can be used to compute Pearson's coorelation coefficient (r) between expression profiles of duplicate gene pairs derived from different modes of gene duplication. Meanwhile, this pipeline can automatically generate 10,000 random gene pairs and compute r values for them.

• Perl
• Python 2.7
  • Pandas
  • Scipy

git clone https://github.com/qiao-xin/Scripts_for_GB.git

Before running this pipline, some data files should be prepared:

For example, we peformed Kallisto to quantify expression abundance of the transcripts in different tissues of Arabidopsis thaliana using RNA-seq reads generated in a previous study (Wang et al. 2016).

The result files were provided in example_data:

• example_data
  • output1
  • output2
  • output3
  • output4
  • output5

The duplicate gene pairs identified from different plants are available on PlantDGD.

Here, we only estimated r values between expression profiles of tandem gene pairs in A. thaliana. Also, you can include other types of duplicate gene pairs (e.g. WGD, PD, TRD) in current directory.

Once the required files have been prepared, try running this pipeline on the example data.

USAGE:

perl compute_pearsonr_pipeline.pl

The integrated spatial expression for each gene in different tissues. The data in alltpm looks like this (tab separated):

GeneID	1	2	3	4	5
AT1G09645.1	89.2424	58.1628	73.8257	79.6055	5.44928
AT5G02280.1	18.9473	24.7855	28.309	33.0487	0.923299
AT1G70700.1	477.756	183.034	181.575	20.1834	7.17899
AT1G25097.1	0.694941	0	0	0	0
AT2G30410.1	77.7176	95.5345	127.086	87.8365	4.49006

This pipeline can extract expression values (measured as TPM) from different tissues (Kallisto outputs) for each gene, and then merge into one file.

Log10-transformed TPM values for each gene.

GeneID	1	2	3	4	5
AT1G09645.1	1.95057124127048	1.76464530561024	1.86820757354698	1.90094307448557	0.736339123802573
AT5G02280.1	1.277547331526	1.39419768438907	1.45192452842012	1.51915438079804	-0.0346576348116481
AT1G70700.1	2.67920614994061	2.26253177082796	2.25905605283343	1.30499432725574	0.856063348381457
AT1G25097.1	-0.158052065139533	-4	-4	-4	-4
AT2G30410.1	1.89051938067131	1.98016023497532	2.10409771060411	1.94367502222247	0.652252144454283

Pearson's r values for tandem gene pairs.

10,000 random gene pairs were generated for A.thaliana when running this pipeline.

Pearson's r values for 10,000 random gene pairs.

Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH: Gene duplication and evolution in recurring polyploidization–diploidization cycles in plants. Genome Biology 2019, 20:38.