Lnc2Catlas is a database providing assessment about the possible relationship between LncRNAs and Cancers, hosted on lnc2catlas.bioinfotech.org. Currently the database contains 27670 LncRNA transcripts and 33 cancer types. The relationship between LncRNAs and Cancers are evaluated and quantified via SNPs, interactions and expressions. All data can be accessed from browse page and search page. All data used and produced are also available on download page.
In Home page:
1. a search box is located to provide search function and leading the users to search page.
2. The circle graph demonstrates the summary of the number of LncRNAs associated to different cancers. By clicking interesting part of the circle, a more detailed results about the caner will be displayed.
3. A brief description and contact information are available on the footer of the page.
In Browse page:
1.all the results are categorized by cancer types. Several sections descripting the disease and results are shown.
2. The description section provides a brief description about the cancer, which comes from Malacards.
3. The SNP section gives a list of all the SNP considered as cancer-associated including the source information.
4. The Gene section shows the proteins used as cancer-associated, provided by Malacards.
5. The LncRNA section lists all the LncRNAs defined as cancer-associated and how they integrated. The detail button will jump to the detail page of the LncRNA.
6. The WGCNA section illustrate several co-expression network thumbnails, each of which presents a block of the whole network calculated from the expression in tumor. Users can click the picture to get a better view of the network allowing zoom and select. However, due to the large scale of the network, this operation may takes 10s to 1 minute.
In Search page:
a search box and examples are provided. Users can search by LncRNA transcript IDs (ENST id), SNP IDs (rs ID) or protein names (Gene symbol). The search results will be shown in the same page. If the search leads to definite LncRNA, the page will be redirect to LncRNA detail page. Searching by SNP IDs or protein name, a list of LncRNA ranking by corresponding elements and which cancer they are related will be shown. If users type in LncRNA IDs, two table will be shown listing all results, separated by SNPs and proteins.
In Detail page:
1. The Basic Information section provide a brief basic information including a predicted secondary structure.
2. The SNP-structure disruption section lists show this LncRNA is related to different cancers via SNPs and the score evaluating the relationship.
3. The LncRNA-protein interaction section is similar to SNPs section, showing the results calculated based on protein-RNA interactions.
4. The Expression Section provides the average expression level across 33 cancer types.
5. The Co-expression network section shows the subgraph which the LncRNA is located in different cancer co-expression network. Each results can be download via the download button in corresponding section.
6. The GO and pathway analysis section shows the results of GO and pathway analysis of co-expression cluster. Users can select a cancer type in the drop-down box.
7. The publications section presents the publications experimentally supporting the above associations.