Help & FAQ in CRlncRNA

Other than the pre-existing databases that aim at lncRNA and cancer, CRlncRNA has some specific features as follows:

i. Only targeting for cancer, the malignant tumor. In CRlncRNA, we laid the emphasis on cancer (malignant tumor)-related lncRNAs, but not lncRNAs involved in benign tumor (e.g. pituitary adenoma and neurofibromatosis type 1), which are usually localized and do not spread to other parts of the body.

ii. Strict inclusion standard with functional experiment. CRlncRNA only collected lncRNAs that had been validated to be pertinent to cancer pathway or clinic-pathological characteristics in the functionally experimental studies. For those with differential expression demonstrated only by high-throughput data and/or qRT-PCR, they are not included. Besides, lncRNAs which are predicted by bioinformatics are not included either.

iii. Integrating functional studies with high-throughput data. For each cancer-related lncRNA, CRlncRNA not only provided its relevant functional data coming from individual study (like the binding factors/genes of cancer-related lncRNA, the roles of cancer-related lncRNA in cancer development and prognosis), but also integrated its high-throughput data (like the expression profile of cancer-related lncRNA between cancer samples and normal, and the epigenetic modification information of cancer-related lncRNA).

iv. Providing more service. Except the basic tools for browsing, searching and downloading, we also furnish CRlncRNA with advanced search, online BLAST service and Genome Browse Server. Advanced search can combine the multiple keywords for inquiry of the lncRNA-related expression tissue, cancer type, etc. Online BLAST service can make the efficiently sequence similarity searching. Genome browser can check the lncRNA-related genomic annotation (e.g. mutation, expression and epigenetic modification).

The first possible reason is that CRlncRNA only collected lncRNAs that had been validated to be pertinent to cancer pathway or clinic-pathological characteristics in the functionally experimental studies, so you cannot find the cancer-related lncRNAs those with differential expression demonstrated only by high-throughput data and/or qRT-PCR, or just predicted by bioinformatics method. Another possible reason is that the data in CRlncRNA is manually curated, so maybe we have omitted some recently published lncRNAs. You can help us by submitting the data via the contribution page.

In CRlncRNA, we provide two kinds of search services: 'Quick Search' (on the top menu) and 'Search' (in the Search tab). You can use 'Quick Search' to find lncRNAs which have name/alias or tissue-type or cancer-type information that related to the search term entered. You can also use 'Search' to do combined search. For example, you can find lncRNAs which expressed in brain and have relationship with glioma by just inputting 'brain' in 'tissue' input box, and ' glioma' in 'cancer' input box.

CRlncRNA's BLAST service is based on the Django app django-blastplus (A simple Django app to conduct web-based blast+ local alignment search). For more details about BLAST programs and parameters, please visit https://www.ncbi.nlm.nih.gov/books/NBK279675/.

CRlncRNA's genome browser service is based on the Biodalliance, which is a fast, interactive, genome visualization tool that's easy to embed in web pages and applications. For more details about Biodalliance, please visit here: http://www.biodalliance.org/started.html.