# lncATLAS

Shiny is busy...

## Search box:

### Quick start:

Find the subcellular localisation of your long non-coding RNA of interest:

1. Enter the official GENCODE gene name (e.g. Malat1) or ENSEMBL gene ID (e.g. ENSG...) below (max. 3 genes)
2. Check for the ID to appear below and press Go to generate the plots

## Help box:

Search for your lncRNAs of interest and press GO to obtain the plots.

You can select at least 3 genes in both the search and reference inputs. If 3 are selected a high resolution screen is recommended.

### What is being displayed?

LncATLAS displays the subcellular localisation for user-selected lncRNAs. Only GENCODE-annotated lncRNA genes are present, and may be accessed using their identifier (ENSG...) or official Gene Name. The localisation of your selected gene, or genes, will be displayed below for available cell types and cellular compartments. Please note that some plots display data for individual cell types, that may be selected using "Select a Cell Line" button.

This localisation is expressed in units of Relative Concentration Index (RCI) - a comparison of the concentration of a gene, per unit mass of RNA, between two cellular compartments. For more information about how this data was analysed, please consult the "About LncATLAS" tab above.

Raw data for individual genes, or all genes, may be accessed from the "Get Raw Data" tab above.

## Plot 2 - Cytoplasmic/Nuclear Localisation: RCI distribution (all cell types)

Note: In the next plot n indicates the total number of genes in each group and m the median RCI value per group. The group percentile corresponding to each gene is also displayed next to the gene point.

## Plot 3 - Cytoplasmic/Nuclear Localisation: RCI distribution (individual cell type)

### Select a Cell Line:

Nuclear

Cytoplasmic

Note: The blue colouring of the inside area corresponds to the genes with more extreme values than the gene selected. This follows a visualisation purpose to help users see the position of their gene in the distribution.

## Plot 4 - Cytoplasmic/Nuclear Localisation: Comparison with expression (individual cell type)

### Nuclear

Note: When 2 genes present similar values in both axis, one of them might get hidden to avoid problems in readability due to the overlap.

## Plot 5 - Subcytoplasmic, Subnuclear Localisation: K562 cells

Note: Data for chromatin, nucleoplasm and nucleolus in this plot were obtained from a total RNA extraction contrary to the other figures that were obtained with a enriched polyA sample.
Note 2: In the plot n indicates the total number of genes in each group. The group percentile corresponding to each gene is also displayed next to the gene point.

## Retrieve raw data from ENSEMBL IDs

Enter in the box a list of ENSEMBL IDs, coding or non-coding to retrieve the raw values from our database.

### Insert a ENSEMBL gene ID list:

Note that you should wait until a table below the line is generated to download the raw data.

## Basic usage

LncATLAS is an easy to use web-based visualization tool to obtain useful information about expression localization of long non-coding class of RNAs. It is easy to use by just searching your lncRNA of interest in the search box. You can also use ENSEMBL gene IDs to select them. There are also some reference genes with a clear nuclear or cytoplasmatic expression profile. In some plots (3 and 4) you could also select the cell line from the dropdown menu to obtain a zoom into the distributions. Although many genes would have a similar profile among cell lines there might exist small changes. In lncATLAS we provide 6 charts that can be divided into 3 sections:

1. Inspect the cytoplasmic-nuclear localisation of your gene of interest (GOI): a barplot indicating the CN RCI values in each cell line for the selected gene(s)
2. Inspect the cytoplasmic-nuclear localisation of your GOI within the distribution of all genes: distribution of RCI values in each cell line for lncRNAs and mRNAs with the selected gene(s) highlighted
3. Inspect the localisation of your GOI at sub-compartment level: localisation values within distributions for the K562 cell line subnuclear and subcytoplasmic compartments

## Other usages

The 2 major alternative usages for lncATLAS are to download raw data for a single selection of genes that can be done directly on the front page or to download a specific data set from a list of gene IDs in a batch mode. This second feature is in the get raw data tab. After entering the list a  .csv  file with the expression values from the selected genes will be generated. In the input, gene IDs must be placed as a column.

#### Multiple gene selection

In the main page, in the search box, you can enter at least 3 genes by the gene name and for the gene ID input. If more, only the first 3 will be considered.

## Data sources

The data used and displayed in lncATLAS is directly obtained from GENCODE release ( V24 ). and is available through our web site in the download all data button from get raw data panel.
The RCI or Relative Concentration Index has been calculated as follows: $$RCI = \log_{2} (\frac{Fraction_{i} \quad (RPKMs)}{Fraction_{j} \quad (RPKMs)})$$
Being the fraction i the cytoplasm and j the nuclear one for CN RCI shown in most plots. This changes for appropiate subnuclear and subcytoplasmic fractions in the last plot from the K562 cell line. Our intention in representing the subcellular localisation with the RCI is to give a value that represents how more concentrated is a particular gene in one fraction compared to another. It's a flexible approach that permits to compare individual genes easily. All the subcellular compartiments available are shown in the following diagram.

## Contact information

This project has been carried out by Rory Johnson's Lab in the Department of Clinical Research (DCR) of the University of Bern and Roderic Guigo's Lab in the Centre for Genomic Regulation at Barcelona. If you have questions or need further information please open an issue in our github repository.

If you find lncATLAS useful for your research please cite our paper.

Mas-Ponte D, Carlevaro-Fita J, Palumbo E, Pulido TH, Guigo R, Johnson R. LncATLAS database for subcellular localization of long noncoding RNAs. Rna. 2017 Jul 1;23(7):1080-7.

You are free to use any of the generated outputs from this web-site if cited appropriately. This site plots are under the CC BY 4.0 license .