Overview
Best experienced using the browsers Chrome Firefox Safari or IE version (9,10,11)
The main structure of GABC is displayed in Figure 1-1:
Figure 1-1:
Figure 1-1
Get an overview of GABC from the Home page . The Home page is displayed in Figure 2-1:
Figure 1-1:
1. Main functions of the database are provided in menu bar form (boxed in red).
2. A quick search of GABC.
3. Click these images to pages including lncRNAs, lncRNA methylation interaction, differential methylated lncRNAs, SNPs, mutations, miRNA-snp, enhancers and super-enhancers.
4. The brief introduction of GABC.
5. The Jbrowse search of GABC.
6. A description of the picture in 7.
7. Statistics of the curated data in GABC.
8. Click to the next page.
Figure 2-1
Browser
Click "Browser" button and select your interested item. The corresponding results will displayed in the right page.
Browser of "Breast cancer associated lncRNAs" page is displayed in Figure 2-1:
1. Click "Breast cancer associated lncRNAs" button in the drop-down menu of "Browser".
2. The results of "Breast cancer associated lncRNAs".
Figure 2-1
Browser of "LncRNA methylation interaction" page is displayed in Figure 2-2:
1. Click "LncRNA methylation interaction" button in the drop-down menu of "Browser".
2. The results of "LncRNA methylation interaction".
Figure 2-2
Browser of "Differential methylated lncRNAs" page is displayed in Figure 2-3:
1. Click "Differential methylated lncRNAs" button in the drop-down menu of "Browser".
2. The results of "Differential methylated lncRNAs".
Figure 2-3
Browser of "Breast cancer associated SNPs" page is displayed in Figure 2-4:
1. Click "Breast cancer associated SNPs" button in the drop-down menu of "Browser".
2. The results of "Breast cancer associated SNPs".
Figure 2-4
Browser of "LncRNAs with somatic mutations" page is displayed in Figure 2-5:
1. Click "LncRNAs with somatic mutations" button in the drop-down menu of "Browser".
2. The results of "LncRNAs with somatic mutations".
Figure 2-5
Browser of "SNPs on miRNAs" page is displayed in Figure 2-6:
1. Click "SNPs on miRNAs" button in the drop-down menu of "Browser".
2. The results of "SNPs on miRNAs".
Figure 2-6
Browser of "Enhancers of breast cancer" page is displayed in Figure 2-7:
1. Click "Enhancers of breast cancer" button in the drop-down menu of "Browser".
2. The results of "Enhancers of breast cancer".
Figure 2-7
Browser of "Super-enhancers of breast cancer" page is displayed in Figure 2-8:
1. Click "Super-enhancers of breast cancer" button in the drop-down menu of "Browser".
2. The results of "Super-enhancers of breast cancer".
Figure 2-8
Search
How to search GABC by keywords ?
The search page of "Breast cancer associated lncRNAs" is displayed in Figure 3-1:
1. Choose "Breast cancer associated lncRNAs".
2. Input interested lncRNA ID/name.
3. Choose the search type.
4. Select the lncRNA chromosome if you know.
5. Click to submit your request.
Figure 3-1
The search page of "Breast cancer associated SNPs" is displayed in Figure 3-2:
1. Choose "Breast cancer associated SNPs".
2. Input interested SNP id.
3. Select the SNP chromosome if you know.
4. Click to submit your request.
Figure 3-2
The search page of "Differential methylated lncRNAs" is displayed in Figure 3-3:
1. Choose "Differential methylated lncRNAs".
2. Input Gene ID/name or transcript ID/name.
3. Choose the search type.
4. Select the lncRNA chromosome if you know.
5. Click to submit your request.
Figure 3-3
The search page of "Differential methylated lncRNAs" is displayed in Figure 3-4:
1. Choose "LncRNA methylation interaction".
2. Input lncRNA symbol.
3. Click to submit your request.
Figure 3-4
The search page of "Differential methylated lncRNAs" is displayed in Figure 3-4:
1. Choose "LncRNA methylation interaction".
2. Input lncRNA symbol.
3. Click to submit your request.
Figure 3-4
The search page of "LncRNAs with somatic mutations" is displayed in Figure 3-5:
1. Choose "LncRNAs with somatic mutations".
2. Input lncRNA ID.
3. Click to submit your request.
Figure 3-5
The search page of "SNPs on miRNAs" is displayed in Figure 3-6:
1. Choose "SNPs on miRNAs".
2. Input miRNA, gene or snp.
3. Choose the search type.
4. Select the chromosome if you know.
5. Click to submit your request.
Figure 3-6
The search page of "Enhancers of breast cancer" is displayed in Figure 3-7:
1. Choose "Enhancers of breast cancer".
2. Input enahncer or target gene.
3. Choose the search type.
4. Select the chromosome if you know.
5. Click to submit your request.
Figure 3-7
The search page of "Super-Enhancers of breast cancer" is displayed in Figure 3-8:
1. Choose "Super-Enhancers of breast cancer".
2. Input super-enhancer name.
3. Select the chromosome if you know.
4. Click to submit your request.
Figure 3-8
Results&Details
GABC results are organized in a data table, with a single association record on each line. Here, we take the results of "Breast cancer associated lncRNAs" for example.
The results of "Breast cancer associated lncRNAs" is displayed in Figure 4-1:
1. Change items number for each page.
2. Use keyword of each column to filter your results.
3. The chromosome of hit lncRNA.
4. The start location of hit lncRNA.
5. The end location of hit lncRNA.
6. The name of hit lncRNA.
7. The entrez id of hit lncRNA.
8. The hgnc id of hit lncRNA.
9. The ensg id of hit lncRNA.
10. The refseq id of hit lncRNA.
11. The pubmed id of reference for hit lncRNA.
12. The year of reference of hit lncRNA.
13. Click to browse detailed information.
14. Click to change page.
The detailed page of "Breast cancer associated lncRNAs" is displayed in Figure 4-2:
1. Users can get the basic chromosome location information for the hit lncRNA.
2. Users can get detailed name information for the hit lncRNA.
3. Users can get detailed method information for the hit lncRNA.
4. Users can get detailed regulatory pattern information for the hit lncRNA.
5. Users can get detailed function description for the hit lncRNA in related paper.
6. Users can get detailed paper information n for the hit lncRNA.
7. Users can get the biomarker type including drug, circulating and survival.
Figure 4-2
Jbrowse
How to use browse the genomic position of the data stored in GABC?
In the home page, we provide search box linked to Jbrowse page, as displayed in Figure 5-1:
1. Place the mouse over "Jbrowse" button.
2. Input the start location.
3. Input the end location.
4. Select chromosome.
4. Click to submit your request.
Figure 5-1
In the Jbrowse page, users can select their interested tracks, and view its location distribution.
Figure 5-2:
1. Select your interested tracks.
2. The genomic location of each item.
Figure 5-2
Download
The download page is displayed in Figure 6-1.
Figure 6-1:
1. Click to view all available datasets in GABC.
2. Click your interested datasets to download.
Figure 6-1