WebHERV

This website (available also as a standalone program) enables you to test for proximity of human endogenous retrovirus (HERV) and HERV-like sequences in the genome to differentially expressed genes, the latter uploaded either as genome coordinates or Affymetrix microarray IDs

SettingsDescriptions
The 'Area' defines the region around the genome coordinates or probe set coordinates in which the program will search for HERV sequences.
  • Area 'overlap': the program will search for HERV sequences upstream and downstream of the probe set or genome coordinates.
  • Area 'downstream': the program will only search for HERV sequences downstream (3') of the probe set or genome coordinates.
  • Area 'upstream', the program will only search for HERV sequences upstream (5') of the probe set or genome coordinates.

'Distance' defines the region (in base pairs) of the DNA around the probe set or genome coordinates which is analyzed for presence of HERV sequences. It is possible to enter a comma-separated list of values to analyze multiple distances at once (e.g.: 100, 1000, 10000).

The 'Minimal sequence length' is the length that a (putative) HERV-derived sequence must have.

The "Maximal HERV e-value" is the expect value that is allowed for sequences to be considered as HERV derived.

Please select only Genome coordinates OR Probe set IDs for upload.

NOTE: delete all uploaded files to switch to another upload tab.


'Genome' allows the selection of different genome versions (currently available: HG18, HG19, RepeatMasker LTRs HG19) for the coordinates of HERV-like sequences.
Here you can upload genome coordinates of your differentially expressed genes in the selected genome version (HG18, HG19 or RepeatMasker LTRs HG19).
  • Each line must contain only one genome position.
  • Format: chromosome[TAB]start[TAB]end[TAB]strand.
  • chromosome: chr1, chr2, ..., chrY.
  • strand: 1 or -1.
  • Press 'Choose' to select a file.
  • Press 'Upload' to upload the files.
Choose
Example genome coordinates file:
  • Example_coordinates_B : genome coordinates of probe sets up-regulated in normal blood cells in comparison to Hodgkin lymphoma cells.
  • Example_coordinates_H : genome coordinates of probe sets up-regulated in Hodgkin lymphoma cells in comparison to normal blood cells.