NucMap is a database of genome-wide nucleosome positioning map across species. It is dedicated to collecting, analyzing and storing nucleosome positioning data in all organisms. NucMap provides services on querying and visualizing nucleosome positioning information at single nucleotide resolution. Meanwhile, it also provides some enrichment analysis on interested genes or samples.
In the "Sample Search" page, all samples in specific species will be listed by default when one species was assigned. User can also narrow sample list by searching with keywords about sample material or assay. All raw data in NucMap database were collected from GEO and ENCODE database. Accession id in GEO can also be used to narrow down sample list.
Sample accession id was created in the format XXNucYYYZZ in NucMap database. XXs refers to different species. YYYs are numbered biosamples from same species. Same YYY means materials may come from the same or similar biosamples. ZZs are numbered assays from YYY. Different ZZs indicate that different assay conditions were applied on samples, such as the concentration of MNase, time of digestion, use different capture antibodies.
Nucleosome browser is an interactive browser built to visualize nucleosome positioning information in NucMap. It was developed based on JBrowse. For each species, tracks for raw reads signal and analyzed nucleosome peaks are available for all samples. Users can choose their interested tracks and view any regions across whole genome.
With analysis modules in NucMap, users can analyze nucleosome enrichment at transcription start site (TSS) across samples or different interested gene groups. Both heatmap and enrichment curve are available in the analysis module.
Yes. User can upload all type of data for side-by-side analysis in the nucleosome browser. The only prerequisite is that, the file(s) to be uploaded should be based on the same reference genome as the one used in NucMap. In NucMap, genome assembly version for each species can be found in this table.
Generally, there is no restriction with interested gene names. However, it is very tricky in which kinds of names to be used. Enrichment analysis mainly focus on nucleosome density around transcription start site(TSS). Typically, one gene may have multiple transcripts with different TSSs. If gene name was used, such as Tp53, Med14 and so on, the most upstream TSS will be used in the enrichment analysis. If users want to check some specific TSSs, it will be better to use transcript names to replace gene names. Meanwhile, all species in NucMap are using annotation from RefSeq, and the excel files for gene names vs transcript names are available for all species on the download page. If some transcript names or gene names don't not match to the name in NucMap database, a caveat will be added to the analysis module page.
The customized gene list should be a tab-separated table. The first column should be gene names or transcript names and the second column is gene group name. if user want to classify all genes into different groups, this column will be labels for different groups. The group names are up to users’ purpose, and they could be “high expressed gene” or “low expressed gene”, “housekeeping gene” and so on. This column is optional. If the second column is not provided, all gene will be treated as the same group. Here is an example of customized gene list (Species: Mus musculus, Sample:mmNuc0020101).
Genomic regions should be formatted as a BED file. One difference with standard BED file is that the 4th column will be borrowed as group name. In each region file, max 6 different group names will be allowed. According to the strand, center will be used and extended by the size defined by region range (upstream and downstream) in the computational process. If only the first three columns were provided, all regions will be treated as “default_group”. If the 6th column was missed, the strand will be treated as “+”. Here are three valid examples:
Example 1: full Bed file.
chr1 3451234 3459876 group1 0 +chr2 1242357 1248769 group1 0 +chr4 6548912 6550123 group2 0 +chr2 3251945 3254589 group3 0 +
chr1 3451234 3459876 group1chr2 1242357 1248769 group1chr4 6548912 6550123 group2chr2 3251945 3254589 group3
chr1 3451234 3459876chr4 6548912 6550123chr2 3251945 3254589chr2 1242357 1248769
In NucMap, all processed reads signal (in bigwig format) and nucleosome peaks can be freely downloaded from the page Download.