What gene coexpression represents

The historical tutorial describes coexpression as similarity between gene expression profiles across samples and conditions. Functionally related genes may be expressed together, so coexpression can help suggest functions for poorly characterized genes. The tutorial uses Pearson's correlation coefficient as a measure of this relationship.

Use the archived gene lists to examine highly ranked partners, retaining the platform and release version. Coexpression is evidence for an association; it does not by itself establish a molecular mechanism.

Expression data and release versions

The historical History page identifies RNA-Seq as the source for the three C. reinhardtii releases: 137 samples for Cre-R1-13-10, 180 for Cre-R1-15-02 and 172 for Cre-R1-15-08. It attributes these to SRA, with project-group data also mentioned for the 180-sample version. The later release removed redundant samples. The two C. merolae releases used 75 and 48 microarray samples from GEO.

Gene models and sample sets differ between releases. The original publication provides the analysis and evaluation methods; the restored documentation does not reconstruct or rerun the original calculation pipeline.

Historical cross-species comparison and annotation

The original gene-list pages compared coexpression of ortholog pairs across species. The tutorial says orthologs were defined by reciprocal best BLASTP hits, with Arabidopsis thaliana coexpression obtained from ATTED-II. A dash in that historical comparison indicated unavailable orthologous coexpression data.

Gene Information pages described functional annotations including Gene Ontology, Pfam, PANTHER, KOG, KEGG Orthology and KEGG Pathway, together with coding DNA and protein sequences. Historical sources were Phytozome v10 / C. reinhardtii v5.5, the C. merolae Genome Project and TAIR10; A. thaliana ortholog information supplemented C. reinhardtii annotation. This description does not imply that all those per-gene pages or annotations are included in the linked ZIP files.

Scope and page structure

ALCOdb was created to support functional analysis of microalgal genes. Its original 2014 release covered the green alga Chlamydomonas reinhardtii and the red alga Cyanidioschyzon merolae. The former Data menu led to keyword or gene-ID search and available gene lists, then to three related views: Coexpressed Gene List, Coexpressed Gene Network and Gene Information.

1. Find a query gene. The former search accepted gene identifiers, symbols or keywords; an available gene list provided an alternative entry point. Sequence similarity search was added later.
2. Inspect ranked partners. Coexpressed Gene List ordered partners by increasing MR and displayed corresponding orthologous coexpression where available.
3. Inspect a network. Coexpressed Gene Network displayed a guide gene and its neighbors. The tutorial describes selecting the five strongest partners of the guide and then the three strongest partners of each, with edges controlled by an MR threshold. The historical interface used Cytoscape.js and could save graphs as PNG files.
4. Consult annotations and sequences. Gene Information combined functional annotation, coding DNA and protein sequences, with links to source resources.

The current static archive instead provides downloads and explanations. It does not offer those interactive steps or generate networks.

Tools described in the original tutorial

Expression Profiler

Displayed a gene's expression across experimental samples, with manually curated strain, growth-condition and other sample information. Users could focus on an individual study. The tutorial described support for C. reinhardtii genes.

DEGs Finder

Provided lists of strongly up- or down-regulated genes for selected comparisons, detected using the TCC package. The historical lists included rank, gene ID, description, log2 fold change, p-value, q-value and links to coexpression data, ordered by p-value. The tutorial described support for C. reinhardtii genes.

Network Analyzer

Checked a user-defined gene set for available coexpression data and displayed a network for the supported queries. The tutorial described support for C. reinhardtii and A. thaliana.

All three tools are currently unavailable. These descriptions document the former service and do not offer an executable analysis or a promise of complete archived tool outputs.