WGD gene pair methylation level TADs boundary methylation level TADs boundary gene density Gene compartments judgment OE matrix generation Chromosome interaction-distance WGD gene pair contact score Gene pair contact frequency Conservative TADs analysis
TIPS

Function: Calculate the interaction scores of paralogous gene pairs derived from WGD.
Test data: OE_matrix.txt, WGD_OE_bed.txt, WGD_TPM_GT2_500klg0.txt, WGD_TPM_LT2_500klg0.txt, 500000.
Download link of test file: https://github.com/yangxy2/3Dgenome-file/tree/main/web_test_file.
Input data description:
O/E matrix: observed/expected interaction matrix; No header; 3 columns, separated by tab; From left to right, each column represents bin1 id, bin2 id, interaction frequency;
Matrix bed: No header; 2 columns, separated by tab; From left to right, each column represents chromosome name-bin start coordinate, bin id;
WGD gene list(FC>2): The fold change of WGD gene pairs is greater than 2;The first row is the header; 10 columns, separated by tab; From left to right, each column represents gene 1 name, chromosome name, start bin coordinate, number of bins spanned, gene 2 name, chromosome name, start bin coordinate, number of bins spanned, fold change, Left/Right (The TPM value of gene 1 is greater than ( Less than) TPM value of gene 2);
WGD gene list(FC<2): The fold change of WGD gene pairs is less than 2; Others same as above;
Resolution: The resolution of O/E matrix(integer).