Ortholog Finder Tool v1.6

A unified bioinformatics web tool for exploring evolutionarily conserved proteins across model organisms. Combines multi-database ortholog search with Gene Ontology annotation extension via ortholog-based Venn diagram analysis.

PhD Thesis: Dul, Z. (2019). A system-level approach to identify novel cell size regulators. King's College London. Downloand from KCL Pure website

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📋 Table of Contents

• Overview
• Two Modes
• Model Organisms
• Live Versions
• Installation
• Configuration
• Project Structure
• Data Sources
• Academic References
• History
• Author
• License

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🔬 Overview

The Ortholog Finder Tool was developed as part of a PhD project at King's College London (2013–2018) to systematically identify conserved regulators of cell size across eukaryotic model organisms. It integrates orthologous protein relationships from multiple databases and cross-references them with pathway annotations and genome-wide functional screen data.

Version 1.6 unifies two previously separate tools into a single application:

Previously	Now
Ortholog Finder Tool v1.5	Mode A: Ortholog Search
GeneOntology Extension Tool v1.0	Mode B: GO Extension

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🧬 Two Modes

Mode A — Ortholog Search

Multi-database ortholog lookup with pathway annotations and cell-size screen hit data.

• 5 species: AT, DM, HS, SC, SP
• 6 ortholog databases: HomoloGene, orthoMCL v5, InParanoid v8, eggNOG v4, COG/KOG, PomBase
• Pathway data: KEGG and Reactome annotations per protein
• Screen data: Published cell-size regulatory gene lists (Jorgensen, Moretto, Hayles, Björklund, Neumann)
• Query levels: orth (all orthologs), path (with pathways), same (shared pathways), size_mut1–6 (screen hit filters)
• Output: Interactive sortable/searchable DataTable + CSV download
• Data: 225,000 ortholog pairs across 40 MB of pre-processed flat files

Mode B — GO Extension

Gene Ontology annotation extension via eggNOG ortholog groups, visualized with Venn diagrams.

• 7 species: AT, CE, DM, DR, HS, SC, SP
• 85 GO Slim Generic terms (from GO Consortium)
• Venn diagram types: Classic Venn (2–7 sets) and Edwards-Venn (2–7 sets)
• Configurable threshold: Minimum species co-occurrence (2–7)
• 4 result tables: Filtered hits, expanded list, conserved core, novel annotation suggestions
• Data: 75 eggNOG export CSVs + 12 SVG diagram templates
• Backend: MySQL queries against orthology_databases and geneontology tables

Method — Homology/Membership (H/M) Ratio

The GO Extension mode identifies potential gaps in Gene Ontology annotations by computing an H/M ratio for each GO term within each orthologous group:

1. Ortholog group resolution — Proteins are mapped to COG/KOG orthologous groups via the eggNOG database (v4). UniProt KB accessions serve as the common identifier across all 7 species.
2. GO annotation lookup — For each orthologous group, the tool retrieves GO Slim annotations for all member proteins from the Gene Ontology database.
3. H/M score calculation — For each GO term within a group, the tool computes the ratio of species carrying the annotation (Homology) to the total number of species with members in the group (Membership). A high H/M ratio combined with a missing annotation in one species suggests a candidate for annotation extension.
4. Visualization — Results are presented in interactive DataTables and Edwards-Venn diagrams (2–7 species) showing the overlap and gaps of annotations across the selected species.

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🧫 Model Organisms

Organism	Code	Taxonomy ID	Mode A	Mode B
Arabidopsis thaliana	AT	3702	✅	✅
Caenorhabditis elegans	CE	6239	—	✅
Drosophila melanogaster	DM	7227	✅	✅
Danio rerio	DR	7955	—	✅
Homo sapiens	HS	9606	✅	✅
Saccharomyces cerevisiae	SC	559292	✅	✅
Schizosaccharomyces pombe	SP	4896	✅	✅

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🌐 Live Versions

Tool	URL	Status
Ortholog Search & GO Tool	orthologfindertool.com	Online

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🚀 Installation

Requirements

• PHP 5.6 or higher
• MySQL 5.7 or higher
• Apache or compatible web server

Setup

1. Clone the repository:

   git clone https://github.com/ZoliQua/Ortholog-Finder-Tool.git
   cd Ortholog-Finder-Tool

2. Create .env file from the template:

   cp .env.example .env

3. Edit .env with your database credentials:

   DB_HOST=localhost
   DB_USER=root
   DB_PASS=your_password
   DB_NAME=ortholog
   DB_SOCKET=
   DB_PORT=3306

4. Set up MySQL database:

   For Mode A (Ortholog Search): No MySQL tables required for the core query — all data is file-based (CSV/TSV). The MySQL connection is only used for GeoIP visitor logging (ip2c table).

   For Mode B (GO Extension): Requires orthology_databases and geneontology tables in the orthology database. These contain the ortholog mappings and GO annotation data used by the QueryGO class.

5. Point your web server to the project root and open index.php in a browser.

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⚙️ Configuration

Environment Variables (.env)

Variable	Description	Default
DB_HOST	MySQL hostname	localhost
DB_USER	MySQL username	root
DB_PASS	MySQL password	(empty)
DB_NAME	MySQL database name	ortholog
DB_SOCKET	Unix socket path (optional, for MAMP/XAMPP)	(empty)
DB_PORT	MySQL port (0 = default)	3306

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📁 Project Structure

orthologfindertool-v1.1/
│
├── index.php                → Redirect to main.php
├── main.php                 → Unified router (mode switching)
├── download.php             → CSV export handler
├── dumper.php               → GO batch export (all 85 terms)
│
├── includes/
│   ├── mysql.php            → Database connection (.env based)
│   ├── mylog.php            → Visitor logging (CSV + GeoIP)
│   ├── ip2country.php*      → GeoIP country detection
│   │
│   ├── functions.php        → FajlBeolvas + Lekeres classes (Mode A core)
│   ├── inc_analyzer.php     → QueryGO class (Mode B core)
│   ├── inc_analyzer_dumper.php → QueryGOExport (batch CSV)
│   ├── inc_functions.php    → VennDiagram + SVG_File + helpers
│   ├── inc_variables.php    → Species, GO terms, POST handling
│   │
│   ├── page_landing.php     → Mode selector (landing page)
│   ├── page_ortholog_form.php    → Mode A: query form
│   ├── page_ortholog_results.php → Mode A: results + DataTable
│   ├── page_2_analysis_{species}.php → Mode A: per-species table templates
│   ├── page_go_analyzer.php → Mode B: GO form + results + 4 DataTables
│   ├── page_sources.php     → References page
│   └── page_aboutus.php     → About page
│
├── _dataset/                → Mode A data files (40 MB)
│   ├── ALL_ortholog_dbs_merged.csv   → 225K ortholog pairs (6 DBs)
│   ├── kegg_pathways_uniprot.tsv     → KEGG pathway annotations
│   ├── reactome_pathways_uniprot.tsv → Reactome pathway annotations
│   ├── regular_names.txt             → UniProt ID → gene name mapping
│   └── {AT,DM,HS,SC,SP}_interact_deg2_exp.csv → Cell-size screen data
│
├── source/                  → Mode B source data (15 MB)
│   ├── eggNOG-export-*-7.csv (×75) → eggNOG ortholog group exports
│   └── ortholog_*_sample.svg (×12)  → Venn diagram SVG templates
│
├── output/                  → Mode B generated output (15 MB)
│   ├── eggNOG-export-*-7.csv (×75) → Processed results
│   └── GO*-Venn-Diagram-*.svg (×49) → Generated Venn diagrams
│
├── _query/                  → Mode A pre-computed results (23 MB)
│   └── jsonquery_{species}.txt      → DataTables JSON (per species)
│
├── media/
│   ├── css/unified.css      → Merged stylesheet
│   ├── js/                  → jQuery 1.11.2 + DataTables 1.10.5
│   └── images/              → Logos, icons, organism photos
│
├── _log/                    → Visitor logs (not tracked)
├── .env.example             → Environment template
├── .gitignore
└── LICENSE.md               → GNU GPL v2

URL Routing

URL	Page
main.php	Landing page — mode selector
main.php?mode=ortholog	Ortholog Search form
main.php?mode=go	GO Extension form
main.php?page=source	References
main.php?page=about	About Us

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📊 Data Sources

Ortholog Databases (Mode A)

Database	Version	Date
BioGRID	3.2.112	April 2014
eggNOG	4.0	December 2013
InParanoid	8.0	December 2013
orthoMCL	5	2013
HomoloGene	—	2014
COG/KOG	—	2014

Pathway Databases (Mode A)

Database	URL
KEGG	genome.jp/kegg
Reactome	reactome.org

Additional Databases

Database	Version	Purpose
UniProt	2014_04	ID mapping & protein names
PomBase	V2.19	Pombe↔Human/Cerevisiae curated orthologs
intAct	2013-11-20	Protein interaction data
MitoCheck	ens73	H. sapiens phenotype data

GO Annotation (Mode B)

Source	Details
Gene Ontology	85 GO Slim Generic terms
eggNOG v4	Ortholog group → protein mapping

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📚 Academic References

Thesis

Dul, Z. (2019). A system-level approach to identify novel cell size regulators. PhD thesis, King's College London. KCL Pure

Cell-Size Screen Publications

Species	Publication	Journal	Year
S. cerevisiae	Jorgensen P et al. — Systematic identification of pathways that couple cell growth and division in yeast	Science	2002
S. cerevisiae	Moretto F et al. — A pharmaco-epistasis strategy reveals a new cell size controlling pathway in yeast	Mol Syst Biol	2013
S. pombe	Hayles J et al. — A genome-wide resource of cell cycle and cell shape genes of fission yeast	Open Biology	2013
S. pombe	Graml V et al. — A genomic multiprocess survey of machineries that control and link cell shape, microtubule organization, and cell-cycle progression	Dev Cell	2014
D. melanogaster	Björklund M et al. — Identification of pathways regulating cell size and cell-cycle progression by RNAi	Nature	2006
H. sapiens	Neumann B et al. — Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes	Nature	2010

Gene Ontology

Ashburner M et al. (2000). Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1), 25–29. doi:10.1038/75556

Ortholog & Protein Databases

Powell S, Forslund K, Szklarczyk D, et al. (2014). eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Research, 42(D1), D231–D239. PubMed: 24297252

The UniProt Consortium (2015). UniProt: a hub for protein information. Nucleic Acids Research, 43(D1), D99–D106. PubMed: 25348405

External Code

Library	Version	License
jQuery	1.11.2	MIT
jQuery DataTables	1.10.5	MIT
ip2country by Blagoj Janevski	—	GNU GPL v2

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📜 History

This tool was originally published as two separate web applications during 2015–2018:

1. Ortholog Finder Tool (orthologfindertool.com) — Multi-database ortholog search with pathway and screen data integration. Archived source: ZoliQua/Ortholog-Finder-Tool-Draft

2. GeneOntology Extension Tool (go.orthologfindertool.com) — GO annotation extension via eggNOG ortholog groups with Venn diagram visualization. Archived source: ZoliQua/Ortholog-Finder-Tool-GO

Version 1.6 (November 2025) unifies both tools into a single application with a shared navigation and mode-selection interface. No data or backend logic was changed — only the UI was consolidated.

The git history of this repository preserves the full commit histories of both original repositories.

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👤 Author

Dr. Zoltán Dul Dentist, Phd graduate (2014–2019), King's College London

• 📧 zoltan.dul@gmail.com

Supervisors & Groups

• Prof. N. Shaun B. Thomas — Cell Cycle & Epigenetics Team, Division of Cancer Studies, King's College London
• Dr. Attila Csikász-Nagy — Csikász-Nagy Group, Randall Division of Cell and Molecular Biophysics, King's College London
• Dr. Azeddine Si Ammour — Genomics and Biology of Fruit Crop, Fondazione Edmund Mach, San Michele all'Adige

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📄 License

This project is licensed under the GNU General Public License v2.0.

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Built at King's College London & Fondazione Edmund Mach