Quadrant plot





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Function:
This tool is suitable for correlation analysis between transcriptome and proteome


Input:
1. enter file:
(1)1. Gene expression file (necessary): this file must contains gene ID and its fold change information, additional information such as annotation list can be included. Fold change column must be point out, for example, if the second column is fold change list of gene expression, please enter 2
(2)2. Protein expression file (necessary): this file must contains gene ID and its fold change information, additional information such as annotation list can be included. Fold change column must be point out, for example, if the second column is fold change list of gene expression, please enter 2
(3) 3. If gene ID and protein ID is inconstant, please input an “ID exchange file” to convert IDs.
(4) 4. This tool only support two group comparison (A vs B).
(5) The input file should be a tab-delimited “.txt” file.


Parameters:


fold change threshold screening:

You can set fold change threshold for gene and protein expression. Default threshold for transcriptome is 2 fold, while proteome is 1.2.


Color of each quadrant:

The color of each quadrant can be changed freely.


x、y lab name:

x and y axes label can be customized. No special symbols such as ().


Font scale:

Font size is recommended between 1-2


Output:
1) A-VS-B.annot.all.xls:This table records the information of all genes/proteins in the quadrants, the expression in the transcriptome and proteome, and the functional annotations
2)A-VS-B_1(2、3、4…).annot.xls:In each quadrant table (total 9), the gene/protein information of each quadrant was recorded, and the expression amount and function annotation of the transcriptional group and the protein group were recorded.
3)A-VS-B.associate.png/pdf:Nine-quadrant diagram

Result description:

The resultant scatter plot is divided into nine quadrants, each quadrants represents


quadrant InterpretationInformation worthy for depth analysis
5 The co-expressed mRNA and protein were not differentially expressed The non-differential expression of most genes and proteins
3,7 The expression patterns of mRNA and corresponding proteins were consistent After transcription, the translation level is not regulated or less regulated genes
1,2,4 Protein expression abundance is higher than mRNA Post-transcriptional or translation levels regulate or accumulate proteins
6,8,9 Protein expression abundance was lower than mRNA Post-transcriptional or translational regulation, such as miRNA regulation of target genes leading to inhibition of protein translation
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example :
Input:gene expression file  protein expression table file  ene ID exchange file


Output:
1:out.1.xls~out.9.xls:
     id      mrna_log2fc     pep_log2fc
     LOC103963471    1.101898276     0.311503
     LOC103962876    5.321928095     0.27858
     LOC103934651    1.275634443     0.27858
     LOC103934659    1.275634443     0.27858
     LOC103936009    1.240125108     0.347099
     LOC103967195    1.343904198     0.335712
     LOC103947707    2.948449827     0.264236
     LOC103953799    1.965322499     0.454176
     LOC103962421    2.461233498     0.299831
     LOC103961069    1.435349801     0.435095
     LOC103966887    1.389905653     0.435095
     LOC103964207    1.130873231     0.435095
     LOC103940874    1.248564226     0.313826
     LOC103954750    1.50225405      0.313826
     LOC103940640    2.058594654     0.275007
     LOC103932053    3.212953745     0.267835
     LOC103965100    1.752689946     0.303342
        

2:out.all.xls :
    id      mrna_log2fc     pep_log2fc      part
    LOC103943480    0.888174145770218       -0.279284       6
    LOC103947063    1.05365929938603        -0.027675       2
    LOC103948276    0.843616811653425       -0.027675       5
    LOC103949900    -0.393177102764054      -0.0679388      5
    LOC103937154    -0.0282269636477752     -0.00868224     5
    LOC103967672    0.311623912452433       -0.00868224     5
    LOC103926846    0.549616011345812       -0.153607       5
    LOC103926851    0.636957138359417       -0.153607       5
    LOC103926854    12.240791332162 -0.153607       2
    LOC103926850    12.240791332162 -0.153607       2
    LOC103963573    0.473813850860616       0.108357        5
    LOC103944315    0.135089944181839       -0.0619024      5
    LOC103955166    0.561527605349946       -0.0528949      5
    LOC103927236    1.21369719218565        -0.0499049      2
    LOC103931072    0.798571501299767       0.051024        5
    LOC103948411    -1.52484940356935       0.0482362       8
    LOC103932581    0.00259769602641484     -0.0350469      5
    .   .   .   .    .    .    .
        

3:out.associate.png/pdf :
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