Help (How to use the DBTSS)

1. Main Left Frame Help


  1. Select the species for which the search will be attempted.
  2. For the TSSseq search, set the "Cell" to "TSS Seq". For the cDNA search, set the "Cell" to "Sanger".
  3. Input the query.
  4. For the TSSseq search, Input minimum ppm. For the cDNA search, Input clone/tag number.
  5. See TSSseq Detail Search section , Search result
  6. See SNP Detail Search section


    7. Click to use analytical tools, Brief user manual is written below.
  7. See Non Coding RNA Viewer section.
  8. See Comparative Viewer section.
  9. See Search for TF Binding Site section.
  10. See SNP Search section.
  11. Download out datas from FTP site.
2. TSS Seq Viewer Help
    Search Result
  1. Top Track displays gene infomation and genome position.
  2. Known genes Track displays gene structure , repeat , CpG island and SNP information.
  3. ENCODE Chromatin map Track displays chromatin state segmentation by HMM. ENCODE Project.
  4. At this track user can select the cell type. User can search TSSs for which differential expressions are observed depending on tissue type or culture conditions.

E. This track displays the TSS Seq cluster represented by >=5ppm(parts per million). If the left check box (all condition, ChIP seq, RNA seq) is selected, the corresponding data is visible.


F. Drag your target region, 2 functional buttons. "calculate tag counts" or "zoom" are visible.
Click the button, the data you request is displayed.


G. The under frame displays each sample TSSseq tag number. Click the AP position in the upper frame, highlight the position in the under frame.

3. TSSseq Detail Search Help
    A. Set the Species.
    B. Set the Expressing Cell Type.
    C. Set the Promoter Type.
    D. Set Expression Preference.
    E. Set Expression level.

    F. Option ChIP Seq overlapping.
    G. Option RNA Seq overlapping.
    H. Option SNP overlapping.

    Click "Search" to show results satisfying the specified criteria.
4. SNP Detail Search Help
A. Search for TSSs within *kb from SNP: rsID or Genomic Position.
B. Search for SNPs within NM region.
C. Search for disease related SNP.

Click "Search" to show results satisfying the specified criteria.
Each result is below. Go viwer link to TSS Seq Viewer.
5. Non Coding RNA Viewer Help
  • This page shows the list of all non coding rna region.
6. Comparative Viewer Help
  • Specify target regions by genomic position or NMID. Select up to two additional species for sequence comparisons.
  • Specify the search conditions for non-conserved elements. Click "detail search" to show further detailed search conditions.
  • For magnification, one click to specify the start point (red vertical line) and the next for the end point (green vertical line). Right click to directly specify the degree of magnification.
    TSS information can be switched between Sanger and TSSseq.
7. Transcriptome-Promoter Connectivity Help
    Possible TF binding sites enriched in particular promoter groups are searched.

  1. Click to retrieve drug information.
  2. Search conditions can be specified by the combination of cDNA (Sanger/Solexa) numbers, expression conditions and user specified NM groups.
  3. Click to add "AND" and "OR" boxes.
  4. Click "Search" to show NM groups satisfying the specified criteria.
  1. Prediction conditions of the TFBS search can be optimized.
  2. Click "Search (Target TF)" to show enriched TFBS in the listed NMs.
  1. Click to show the NM list in which predicted TFBS appear.
  2. P-value: Statistical significance of the enrichment evaluated by hyper geometric distributions.
8. Search for TF Binding Site Help
  1. Select the species for which the search is attempted.
  2. Create the box for exact sequence match.
  3. Create the box for matrix search.
  4. Create the tables to specify the search conditions for each TF. (The order of factor 1,2,3... does NOT correspond to the relative positions of the TFs)
  5. Specify sequence pattern or matrix used for the search.
  6. Specify cut-offs and the regions that should be considered (TSS is designated as 0)
  7. Fill all search conditions (TFs in the boxes of same colors are considered as "OR" and different colors are "AND".)
  8. Press to search