Overview

This application transforms the miREA analytical workflow into an interactive scientific web interface.

Users can choose a method, select a biological pathway resource, inspect ranked pathway results, visualize pathway-gene and miRNA-gene patterns, and export outputs for downstream interpretation.

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Real Analysis

Uses precomputed miREA result files and reference-linked edge detail tables.

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Ranked Results

Explore ranked pathway tables and barplots for fast interpretation.

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Interactive Heatmap

Inspect enriched pathways, target genes, miRNA-gene regulatory edges, and expression annotations in one view.

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MGI Table

View detailed miRNA-gene interaction values under the heatmap, including MGI and DEMGI fields.

Tutorial & Example Data

miREA includes 9 analysis methods. Each method has its own input requirements, so Online miREA asks for the method first and then shows only the data that method needs.

Choose a method

Select TG, MiR or Edge analysis in New Analysis.

Upload only what is needed

The upload form changes automatically for the selected method.

Run and interpret

Choose the pathway database, run miREA and inspect tables and heatmap results.

BLCA example data

Use the supplied BLCA example files to test the workflow.

Download All Example Data

Important: four BLCA data types are available, but not every method needs all four.

Possible input data

These are the four data types used in the original BLCA tutorials.

miR_DE Differential miRNA expression analysis result

gene_DE Differential gene expression analysis result

miR_expr miRNA read-count matrix for tumor primary samples

gene_expr Gene read-count matrix for tumor primary samples

Matched matrices: when both read-count matrices are used, miRNA and gene matrices must contain matching sample-column names.

What changes by method?

Online miREA keeps the interface method-specific so users do not need to understand or upload unnecessary files.

Input files: only required data are displayed.
Settings: controls not used by the selected method are hidden.
ORA methods: do not show the permutation-iterations control.
Edge methods: can require additional gene and matched read-count information.

Show original BLCA file paths

gene_DE → data/raw_data/cancer_data/DEG/BLCA_DEG.csv
miR_DE → data/raw_data/cancer_data/DEmiR/BLCA_DEmiR.csv
gene_expr → data/raw_data/cancer_data/paired/BLCA_gene_TP.csv
miR_expr → data/raw_data/cancer_data/paired/BLCA_mir_TP.csv

Method-specific input guide

Use this table only as a reference. In New Analysis, selecting a method automatically shows the corresponding upload fields.

Method	Analysis unit	Required input	Example data
TG-ORA	Target genes of DEmiRs	miR_DE	BLCA_miR_DE.csv
TG-Score	Ranked target genes	miR_DE gene_DE	BLCA_miR_DE.csv BLCA_gene_DE.csv
MiR-ORA	DE miRNAs	miR_DE	BLCA_miR_DE.csv
MiR-Score	Ranked miRNAs	miR_DE	BLCA_miR_DE.csv
Edge-ORA	DEMGI edges	miR_DE gene_DE miR_expr gene_expr	BLCA_miR_DE.csv BLCA_gene_DE.csv BLCA_miR_expr.csv BLCA_gene_expr.csv
Edge-Score	Ranked quantitative MGI edges	miR_DE gene_DE miR_expr gene_expr	BLCA_miR_DE.csv BLCA_gene_DE.csv BLCA_miR_expr.csv BLCA_gene_expr.csv
Edge-2Ddist	Quantitative MGI edges	miR_DE gene_DE miR_expr gene_expr	BLCA_miR_DE.csv BLCA_gene_DE.csv BLCA_miR_expr.csv BLCA_gene_expr.csv
Edge-Topology	MGI edges + network topology	miR_DE gene_DE miR_expr gene_expr	BLCA_miR_DE.csv BLCA_gene_DE.csv BLCA_miR_expr.csv BLCA_gene_expr.csv
Edge-Network	DEMGI-seeded network propagation	miR_DE gene_DE miR_expr gene_expr	BLCA_miR_DE.csv BLCA_gene_DE.csv BLCA_miR_expr.csv BLCA_gene_expr.csv

Design rule: choose the method first; Online miREA then requests only the inputs and settings used by that method.

Status

Analysis Summary

Method

Database

Returned Rows

Top Pathway

Overview

Tutorial & Example Data

BLCA example data

Possible input data

What changes by method?

Method-specific input guide

Status

Analysis Summary

Heatmap Controls

Interactive miRNA-Pathway Heatmap

Table 1: Pathway Results

Table 2: miRNA-Gene Interaction (MGI) Table