Help Content

  1. Work Flow
  2. File Format
  3. Result

1, Work Flow (Top)

The work flow is pretty simple:
1) Upload your file (see File Format Section for the requirements)
2) Check your file format, and
3) If the file meets with the requirements, the user will be notified by email and the analysis will be done in a midnight batch run. If the file format does not meet the requirements, the analysis will stop.
4) See the results and download them (See Result section)

Here are some snapshots for the analysis by TNBCtype server:

1.1 Upload

upload page

1.2 Upload progress bar

progress bar

1.3 File format check procedure

Initially we will check whether the file has been uploaded succesfully and whether it is not a binary format file, then we will check followings:

  1. Whether there exists at least on sample or duplicated samples (no sample or duplicated samples are not allowed and will be stopped)
  2. Whether there exists 'ESR1' gene or duplicated genes (data not including 'ESR1' gene or exists duplicated genes are not allowed and will be sotpped)
  3. Whether there are enough genes overlapped with our background gene set (data with overlapped gene number less than 2000 are not allowed and will be stopped)
  4. Whether there exists ER-positive samples(ER-positive sample means there are more than 75% genes' expression lower than ESR1's in the sample. Data containing ER-positive sample are not allowed and will be stopped)

1.3.1 File format check with success

file format check success

1.3.2 File format check with failure (Data containg ER-positive sample here as an example)

file format check error

1.4 Result

See Result section

2, File Format ( Top)

Currently, we only accept ASCII format file delimated by comma (,),commonly know as csv format. The first line of the file is the sample name and the first column of the file is the Human Gene Symbol (e.g, P53, NAT2). The remaining columns are the expression values for each gene at each sample.

An example file is available here and a discription of the file format is shown below:

file format

3, Result (Top)

The result consists of 4 parts:
1) Running time information;
2) Download section (both uploaded data and result data);
3) Table representation of the result with different colored rows;
4) Graph representation of the result.

Here is an example of the snapshot of result:

Result snapshot

Center for Quantitative Sciences
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