CNAdbCC

   1. The type of input dataset

   2. Query by sample ID

   3. Query by gene symbol

   4. Query study by Browse table

The detection of cervical cancer copy number variations(CNVs) is based on copy number segmentation data, which can be generated by array Comparative Genomic Hybridisation (aCGH) or Single Nucleotide Polymorphism (SNP) array platforms. Herein, The type of input data required include the sample ID, chromosome number, start and stop positions of each segment, and normailzed signal intersity. Uers can input sample name from GEO or TCGA. Table 1 indicates an example of the input sample format and content.

Table 1. The sample content of input data.

CNAdbCC contains about 1000 preprocessed cervical cancer CNVs samples . All data were collected from NCBI Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Uers can explore sample of interest in the search box on 'Search' page, and customize the threshold and color of copy number alterations.

Figure 1. The interface of the sample data query.

(1) Input sample ID to investigate the CNVs of the specific sample. All study can view on 'Browse' page.
(2) Parameters and thresholds to call genomic gains and losses. The default values are 0.15 and -0.15.
(3) Set color for genomic gains and losses. The default color are Red and Blue.

Figure 2. An example of sample data query result.

(1) Received the sample name.
(2) The sample copy number alterations for the whole genome.
(3) The sample copy number alterations for each chromosome (eg: chr 1, chr2).
(4) Input start and end genomic positions (Mb) to zoom in on particular region. It can link to UCSC database.

By querying a specific gene name, uers can investigate the copy number alterations of gains, losses and normal in the whole samples, respectively. Then, specific gene aberration information are obtioned for subsequent analysis,

Figure 3. The interface of gene data query.

(1) Input gene symbol (eg: PIK3CA, EP300).
(2) The entire list of genes that can be used for analysis.
(3) Set color for copy number gains losses and normal. Click 'search' to view result.

Figure 4. An example of gene symbol query result.

(1) Diagram of genes on chromosomes.
(2) The basic informations of selected genes.

Figure 5. An example of gene symbol query result.

(1) The gene symbol of the user entered.
(2) The proportion of copy number gains, losses and normal, respectively.
(3) The samples of copy number gains and losses in selected series.

There are 16 preprocessed GEO or TCGA data series integrated into CNAdbCC. Click on the study title and the related genomic alteration data will be displayed, include corresponding sample information, author information, article report and sample quantity.

Figure 6. The interface of study query and information.

(1) The series name, click it, will connect to the GEO databaes.
(2) Main information of each study. click it, the database wil return a detailed study information page.
(3) The pubmed ID of the study, click it, will connect to the study acticle from NCBI.

Figure 7. An example of the study data visualization interface

(1) The general information of the selected data series.
(2) Visualization option including threshold and color.
(3) The frequency plot of copy number alterations for the selected data series.