With ASMdb, experimental biologists can easily explore the BS-Seq datasets (GEO), search for DNA methylation levels in different tissues, find answers for their questions, and test their hypotheses.
1. Browse and search allele-specific DNA methylation regions (ASMs).
2. Browse and search DNA methylation profiles across different samples.
3. Gene meth profile across samples.
4. Allele-specific expressed gene.
5. Browse DNA methylation results in cancer.
6. Differentially methylated genes in cancer.
7. High frequency allele genes in cancer.
8. High frequency allele genes in species.
9. Browse Differential DNA methylation (DM) results in 'Genome Browser'.
The more details of using ASMdb please refer to: ASMdb-tutorial.pdf
If you have any questions, please contact us in time.
ASMdb shows the information table of allele-specific DNA methylation detected in the samples, and users can search and view the ASMs to verify the experimental design.
Users also can view the table of the ASM results.
In DNA methylation profile module, users can easily search for DNA methylation levels in different tissues.
Display the DNA methylation level of a specific gene in a species in the form of pictures (histogram and line chart) and tables.
Users also can easily search for DNA methylation levels of genes/promoters in different tissues.
The gene expression in cancer is obtained from 'GEPIA2'
Allele specific expressed genes can cause different phenotypes of individuals and are associated with diseases and other important biological functions. We identified SNP information through the corresponding DNA methylation data, and then identified allele specific expressed gene through SNP information and RNA-Seq data.
ASMdb shows the information table of allele-specific expressed genes detected in the samples, and users can search and view the allele-specific expressed genes to verify the experimental design.
We show the allele specific expressed genes in the form of table, and the gene link of the GEPIA2.
In Gene meth profile in cancer module, use can easily search for DNA methylation around in tumor.
And you can view the gene methylation level in tumor and normal data.
As far as we know, compared with normal tissues and cancer tissues generally have abnormal methylation levels. Therefore, in this database, we compared the methylation levels of genes in normal and cancer tissues, and obtained differentially methylated genes in different types of cancers.
Here is the result page of differentially methylated genes in brain cancer.
7. High frequency allele genes in cancer. Back to top goto ASMdbRecent studies have shown that ASM is increased in cancers, such as, lymphoma, Myeloma. As we all know, ASM is one of the main causes of imprinted genes, altered DNA methylation level of imprinted genes has been implicated in a range of cancers. At the same time, the allele-specific expression is essential for the occurrence of diseases and the treatment of cancer. Therefore, we counted the high frequency ASMG /ASEG in cancer.
In this part, we show the distribution of high frequency ASMG/ASEG in the whole genome with various cancers. The high frequency ASMG/ASEG list is showed in table. And the above results are showed in lung cancer.
8. High frequency allele genes in species. Back to top goto ASMdbAs we known, the ASM and ASEG are important functional elements in various species. Therefore, we counted the high frequency ASMG/ASEG in various species.
In this part, we show the distribution of high frequency ASMG/ASEG in the whole human genome.
9. Browse DNA methylation results in 'Genome Browser'. Back to top goto ASMdbMethylation of HOX5 gene may result in the loss of its expression and, since the encoded protein upregulates the tumor suppressor p53, this protein may play an important role in tumorigenesis. (http://www.cancer-genetics.org/HOXA5.htm)
ASMdb also provided the expression levels of cancer related genes in different cancers, which was derived from GEPIA2 (http://gepia.cancer-pku.cn/).
The DNA methylation level in liver cancer:
The DNA methylation level of prostate related gene PITX2 (Pidsley, Ruth et al. 2018) in Genome Browser:
DNA methylation levels in MET1, drm1 / 2, dcl2 mutants in Arabidopsis thaliana:
In Identify CpG islands module, users can easily detect CpG islands in FASTA sequence.
In many cases, researchers eager to check the DNA methylation level of a gene of interest. We provide this function in this module. You only need to provide the species name and gene id to quickly display the methylation level of the gene in part1. What’s more, if you just want the figure which can nest into other website, we also provide this function in part2.
If you want to quickly compare the methylation levels of genes in normal and cancer tissues, you only need to provide the tissue (such as Blood, Brain and so on), cancer or disease (such as ALL, cancer and so on), gene id (such as HOXA5 and CTCF and so on). The list of tissue and disease that you can select are shown in part3.