NCI RID Tools
- ISmapper
- ISmapper is a program designed to map retrovirus integration sites to their host genes. The program displays provirus LTRs in the context of the host genome to facilitate PCR primer design and to aid cloning of the inserted provirus. This is a standalone tool. The submitted file will not be stored in the database.
- To use this tool, users need to
- Select the virus from the virus pull down menu
- Upload a text file containing the original ID, chromosome number, integration site, LTR, and provirus orientation in each line. For example:
| original_id | chr | insert_position | LTR | insert_orientation
|
|---|
| 1 | chr1 | 15009253 | 3LTR | +
|
| 2 | chr9 | 13555399 | 5LTR | +
|
| 3 | chr6 | 3430489 | 3LTR | -
|
Note: The first line must be column names (as shown above); Each item should be separated by a tab.
- Click submit.
- To display the integration site and the flanking host sequences, click "I" button in the result page.
- Please limit the number of input sites to < 200, 000.
- VIGE -- Virus integration and host gene expression analysis
- VIGE is a tool used to display the distributions of virus integration sites and host gene expression level.
- To use this tool, users need to enter their own gene expression data and provirus integration data, or select a sample from the list.
- To use your own data, two files need to be uploaded. Each file, the gene expression data file and the integration data file need to be in tab delimited text files.
The format of the gene expression file:
| Gene name | Chromosome | MID | TSS | TEND | Expression |
|---|
| MIR1302-10 | 1 | 30332 | 29554 | 31109 | 0 |
| FAM138A | 1 | 35318 | 34554 | 36081 | 26 |
| OR4F5 | 1 | 69550 | 69091 | 70008 | 66 |
| RP11-34P13.8 | 1 | 90328 | 89551 | 91105 | 24 |
Note: MID: middle point of gene transcript location; TSS: Transcript start site; TEND: Transcription stop site.
The format of Virus integration site file:
| Chromosome | Integration site |
|---|
| 1 | 568829 |
| 1 | 718597 |
- This tool has 3 options
- Full chromosome: this option will display integration sites and gene expression in a full length chromosome. To use this option, users need to select a chromosome.
- Partial chromosome: this option will display integration sites and gene expression within a range of a chromosome. To use this option, users need to select a chromosome, enter a start position and an interval in million bases.
- A specific gene: this option will display integration sites and gene expression for a specific gene. If users leave the flanking region blank, the exact length of the selected gene will be displayed. If users enter a flanking region in million base, the selected gene and its flanking region will be displayed. To use this option, leave chromosome, start position, and interval blank.
If there are any questions, please contact Mary Kearney, Ph.D at rid@mail.nih.gov
