Welcome to MAP², the microRNAs Analysis Portal.
MAP² is a resource for mining and analysing microRNA-related -omics data. Datasets are pulled from both NCBI Gene Expression Omnibus and EBI ArrayExpress; once selected, MAP² offers the right tools to conduct exploratory and in-depth analyses on molecular data obtained from both tissues and cell lines.
How MAP² is built
MAP² is powered by SMAC, an automated data selection and retrieval system implemented by our group. Publications of interest and the molecular data attached to them are identified from PubMed: GEO identifiers and ArrayExpress accessions are used to establish computational links between the literature and any associated data. When data is available in the public domain, the system downloads the underlying expression matrices and feeds them into the relevant analytical pipelines. The processed outputs are then served by MAP² on the per-publication and per-dataset pages.
What you can do
Once you select a publication that carries GEO data, you can run (and download) multiple analyses, both pre-computed by the pipeline and live on a user-chosen subset of samples:
1. Explore the literature
Filter the microRNA-related publications by year, journal, MeSH terms, keywords, free text and by which pre-computed analyses are attached. Papers with GEO data carry a data ↗ chip; filter dropdowns refresh their counts live as you tick filters elsewhere.
Open Explore →2. Inspect a dataset
For a paper with attached data, browse the GEO sample table, the pre-computed PCA / correlation / enrichment outputs and — when the cohort includes breast-cancer samples — an interactive panel showing receptor status and a tumour-purity proxy.
Browse datasets →3. Live subset analysis
Select samples in the metadata table and run PCA, a clustered heatmap, gene–gene correlation, a per-gene expression boxplot, or a directed gene-interaction network on just those columns — all server-side, sub-second on typical datasets.
User guide →Companion tools
Two specialised tools live next to the literature browser. Both take FASTA-style miRNA input and return a results page you can download from.
MirCompare
Align plant miRNAs against host (mammalian) miRNAs using a two-tier scheme (whole-sequence + seed). Filtered hits are joined to DIANA-TarBase v9 validated targets and run through Enrichr (KEGG, GO BP, Reactome, WikiPathways) — all on the same results page.
Open MirCompare →
COMPASS
Score exogenous miRNAs directly against human gene 3′ UTRs with a sequence-based machine-learning classifier. Trained on experimentally-validated miRNA-target interactions using seed-site features, ViennaRNA duplex MFE and phyloP conservation; returns a ranked shortlist of predicted human targets per exogenous miRNA.
Open COMPASS →What's new
MAP² is a complete rebuild of the original MAP. The biological analyses you knew are all still here; what you'll notice as a user:
- More datasets behind every paper. MAP² now looks at both NCBI GEO and EBI ArrayExpress for the expression data attached to each publication, giving you broader underlying coverage.
- More accurate paper-to-data links. A dataset is shown next to a paper only when that paper is recorded as the dataset's primary publication. Reviews and meta-analyses no longer show up tagged with dozens of unrelated datasets.
- Live, context-aware filters. On the Explore page, ticking a journal, year or MeSH term immediately narrows the values shown in the other dropdowns, so you can see at a glance how much corpus remains under your selection.
- Cleaner keyword and MeSH lists. Generic terms (microRNA, Humans, Animals, Female, Male, Mice, Adult …) are stripped from filters and stats, and variants like "biomarker / biomarkers / Biomarker" are grouped into a single concept so each one appears once with the right total.
- Dedicated statistics page. Top journals, keywords, MeSH terms, year distribution and dataset counts by analysis type, all in one view.
- Interactive breast-cancer profile. Receptor status (ER, PR, HER2) and tumour purity are now zoomable, hoverable charts instead of static images. The receptor calls read the relevant genes directly, fixing cohorts that used to come back as "all samples unknown".
- Richer MirCompare results. Every plant ↔ human cross-kingdom hit now lists the host miRNA's experimentally-validated target genes and a pathway-enrichment panel (KEGG, GO Biological Process, Reactome, WikiPathways) — all on the same results page, downloadable as TXT/CSV.
- Works on phones and tablets. The navigation collapses to a menu icon and the Explore table stays readable on small screens.
- Always up to date. MAP² fetches new papers and refreshes analyses every night automatically. You don't need to do anything to see the latest content.
A more detailed walk-through — including the two features intentionally not carried over from the legacy site — is on the User guide page.