How to make search in CAPRIS Database
There are two different databases in CAPRIS webpage. Motif search contains the information for cancer gene groups which are clustered according to the gene's selected promoter region and their predicted motifs. Gene Resources contains all the final extracted genes from CancerGene Database with it's gene ID, name, cancer type(s) and promoter region
Motif Search
For looking into genes in gene groups, mainly there are two kind of search options: Gene Characteristics or Sequence Search. It is allowed to make search only in one field. Both of the fields can be filled but in submit only the selected option will take into evaluation. Gene Characteristics symbolizes three denomination of gene as Gene ID ( i.e. NM_000059 ) , Gene Name ( i.e. BRCA2 ) and Cancer Type ( i.e. Breast ). Again only one field can be selected and when Cancer Type option is selected, a list of all cancer types come into screen to be selected ( Figure 4.1 ). Gene ID and Gene Name fields are not case sensitive and the written word will be looked in as inner search.
Figure 1 Cancer Type List
When one of the options is filled, the matched group genes are printed on screen with Group IDs and genes which belong to these groups( Figure 4.2). Searched material will be labeled red on the this pages. Clicking on the Group ID will open that Group with it's genes and extracted motifs by MEME (Figure 4.3). There are two choices in this last page is that the motif ,whose length is more than 15 bp, can be taken into BLAST by getting motif to BLAST webpage. The second chance is to look over the gene sequences by clicking the desired gene's ID.
Figure 2 Searching for 'BRCA2'
Figure 3 Group details with genes and motifs
Sequence search can be done in four options: Inner Search, Exact Match, Start With, End With. Searched sequence should contain only A, C, T, G (search is not case sensitive) letters and space (Figure 4.4). If the sequence length is more than 20 bp, BLAST is used to look for matches between database motifs and searched sequence (Figure 4.5) else only the sequence itself is searched in database according to search option. Clicking on resulting Group ID's will show us the matched part of motif by labeling it in red. (Figure 4.6)
Figure 4 Search for Sequence
Figure 5 Blast Search and Results
Figure 6 Group ID 127 and BLAST matching sequence
Gene Resource
Like in the Motif Search our gene database can be searched in Gene Characteristics.It is allowed to make search only in one field. Gene Characteristics symbolizes three denomination of gene as Gene ID ( i.e. NM_000369 ) , Gene Name ( i.e. TSHR ) and Cancer Type ( i.e. Breast ). Again only one field can be selected and when Cancer Type option is selected, a list of all cancer types come into screen to be selected ( Figure 4.7 ). Gene ID and Gene Name fields are not case sensitive and the written word will be looked in as inner search.
Figure 7 Cancer Type List
When one of the options is filled, the matched genes are printed on screen with Gene IDs, Gene Names and Cancer Types (Figure 4.8).Searched material will be labeled red on this page. Clicking on the Gene ID will open that gene with it's gene id, name, all related cancer types and -500 +100 promoter region (Figure 4.9).
Figure 8. Searching genes in Database related to Breast Cancer
