3. Functional Requirements

3.1. Input

A valid submitted gene expression file has the following format:

• It is a TAB-delimited, plain text file with three columns;
• The file contains an optional head line, followed by each gene’sexpression in a control sample (e.g., ControlSample) and in a treatment sample(e.g.,KnockOutSample).

See the txt file pattern as following:

gene_id	ControlSample	KnockOutSample
AT1G01010	1.198558083	2.036161827
AT1G01020	13.75736234	13.370796
AT1G01030	0.833779536	0.203616183
AT1G01040	9.58846466	7.126566394
AT1G01046	0	0
AT1G01050	23.81482799	21.10821094
AT1G01060	0.625334652	1.221697096
AT1G01070	1.719670292	0.950208853
AT1G01080	28.34850421	25.24840665
AT1G01090	58.26034505	42.96301455
AT1G01100	1066.508249	1308.030358
AT1G01110	2.709783491	1.425313279

3.2. Output(Data Analyzing)

The web application displays a table and a scatter plot when given a gene expression file.

3.2.1. Table Analyzing

The table contains a list of differentially expressed genes with the following format:

gene_id	control_sample	knockout_sample	log_2[FC]
AT1G01010	1.198558083	2.036161827	0.76

3.2.2. Plot Analyzing

The scatter plot displays differentially expressed genes. The X-axis is Control, and Y-axis is KnockOut. Replace ‘Control’ and ‘KnockOut’ with appropriated column names if provided in the uploaded file. The up-regulated genes are shown in red dots, and down-regulated genes are shown in blue.