AlgaePath 2.0 is a web-based database integrating gene information, biological pathways, and next-generation sequencing (NGS) datasets derived from Chlamydomonas reinhardtii and Neodesmus sp. UTEX 2219-4. By using Gene Search, Pathway Search, DEGs Search, Enrichment Analysis, and Co-expression Analysis in AlgaePath, users can effectively identify transcript abundance profiles and compare variations among different conditions in a pathway map.

EXPLORE

Gene Search

Provides basic gene information as well as the expression level data under different conditions.

Expression Profiles

Displays gene expression levels across selected conditions using line charts and heatmaps, based on a gene set.

Pathway Search

Provides basic information on various KEGG pathways and gene expression data.

DEGs Analysis

Provides differentially expressed genes between two customized conditions.

Enrichment Analysis

Provides information on pathways and Gene Ontology (GO), along with transcript abundance levels of genes under different conditions.

Co-expression Analysis

Co-expression genes are provided based on Pearson's correlation coefficient (PCC) or Spearman's rank correlation coefficient.

Guide

Gene Search

  1. Gene basic information(gene deacription、sequence、KEGG pathway and GO trem).
  2. Transcript abundance level.

Expression Profiles

  1. Provide comparison of gene expression.

PATHWAY SEARCH

  1. Provide enzyme expression in specific conditions within the KEGG pathway.
  2. Identify the co-occurring TFBS and their binding sites within the promoters of gene groups in the KEGG pathway.

DEG SEARCH

  1. Compare differentially expressed genes between different conditions.
  2. Gene groups with increased or decreased expression to perform GO/pathway enrichment or promoter analysis.

PATHWAY / GO ENRICHMENT ANALYSIS

  1. Identify which GO terms or KEGG pathways are enriched in a group of genes.

CO-EXPRESSION ANALYSIS

  1. Identify which genes co-express with a gene under different condition groups.
  2. Identify the co-expression relationships among a group of genes.