SOORENA
Publication & Metadata
Proteins & IDs
Model Confidence
SOORENA
Dataset Statistics
Based on current filters
Total Matching Papers
Source Mix
Autoregulatory Types
Publication Timeline
Top Journals
Mechanism Probability Distribution
Type Confidence Distribution
Model Training Performance
Performance metrics from the published SOORENA study
Stage 1: Binary Classification (n = 600 test samples)
Stage 2: Multi-class - Overall Performance
Stage 2: Per-class Performance
Source: bioRxiv preprint doi: https://doi.org/10.1101/2025.11.03.685842
SOORENA
Autoregulatory Mechanisms Ontology
A structured classification of self-directed biochemical processes identified and categorized by the SOORENA pipeline.
Hierarchical Structure
Mechanism Definitions with Ontology Relations and Citations
1. Autocatalytic Reaction (+)
A chemical reaction in which its product or intermediate accelerates the same reaction. Supports nonlinear self-reinforcement and chemical self-organization.
Synonyms
self-catalysis, autocatalysis, self-reinforcing reaction
Antonyms
heterocatalysis, enzyme-catalyzed
Related Terms
chemical oscillation, nonlinear dynamics
Core Ontology Relations
- is-a: chemical reaction
- has-input: reaction substrates
- has-output: product that acts as catalyst
- enables: self-amplification in reaction networks
- occurs-in: biochemical and chemical systems
Key References:
- Blackmond D. G. (2009). Angewandte Chemie International Edition , 48, 6092-6101.
- Plasson R., Brandenburg A., Jullien L., Bersini H. (2011). Chemical Society Reviews , 40, 2005-2018.
2. Autophosphorylation (+)
A protein kinase phosphorylates its own amino acid residues (cis or trans), tuning its conformation, catalytic activity, localization, and signaling dynamics.
Synonyms
self-phosphorylation, cis-phosphorylation, intramolecular phosphorylation
Antonyms
dephosphorylation, heterophosphorylation
Related Terms
autokinase
Core Ontology Relations
- is-a: protein self-modification event
- part-of: post-translational regulation
- regulates: kinase activity and activation state
- has-input: kinase + ATP
- has-output: phosphorylated kinase + ADP
- occurs-in: bacteria, plants, animals
Key References:
- Reinhardt R. et al. (2023). eLife , 12, e88210.
- Xu Q. et al. (2015). PNAS , 112, 11753-11758.
3. Autodephosphorylation (–)
The process by which a protein removes phosphate groups from itself, typically through intrinsic phosphatase activity or conformational changes that reverse autophosphorylation.
Synonyms
self-dephosphorylation, autophosphatase activity, intrinsic phosphatase
Antonyms
autophosphorylation, heterophosphatase
Related Terms
autophosphorylation, phosphatase activity
Core Ontology Relations
- is-a: protein self-modification event
- part-of: post-translational regulation
- regulates: phosphatase activity and deactivation
- has-input: phosphorylated protein
- has-output: dephosphorylated protein + Pi
- related-to: autophosphorylation (reverse process)
Key References:
- Related to intrinsic phosphatase activity in dual-function kinases
4. Autoacetylation (+)
The process where an acetyltransferase acetylates itself, adding acetyl groups to its own lysine residues, often affecting protein activity or stability.
Synonyms
self-acetylation, cis-acetylation, intrinsic acetyltransferase activity
Antonyms
deacetylation, heteroacetylation
Related Terms
histone modification, lysine acetylation, protein acetylation
Core Ontology Relations
- is-a: protein self-modification event
- part-of: post-translational regulation
- regulates: acetyltransferase activity and protein function
- has-input: acetyltransferase + acetyl-CoA
- has-output: acetylated protein + CoA
- related-to: histone modification, lysine acetylation
Key References:
- Related to intrinsic acetyltransferase activity
5. Autodemethylation (±)
The process by which a protein removes methyl groups from itself through intrinsic demethylase activity, reversing the effects of methylation.
Synonyms
self-demethylation, intrinsic demethylase activity
Antonyms
automethylation, heteromethylation
Related Terms
protein methylation, demethylase activity, epigenetic regulation
Core Ontology Relations
- is-a: protein self-modification event
- part-of: post-translational regulation
- regulates: demethylase activity and epigenetic state
- has-input: methylated protein
- has-output: demethylated protein
- related-to: protein methylation, epigenetic regulation
Key References:
- Related to intrinsic demethylase activity
6. Autoubiquitination (–)
An E3 ubiquitin ligase attaches ubiquitin to itself, altering its stability, proteasomal targeting, and signaling functions depending on chain type and site.
Synonyms
self-ubiquitination, cis-ubiquitination, auto-ubiquitylation
Antonyms
deubiquitination, heteroubiquitination
Related Terms
protein degradation
Core Ontology Relations
- is-a: protein self-ubiquitylation
- part-of: ubiquitin–proteasome regulatory system
- regulates: E3 ligase abundance and pathway output
- has-input: E3 ligase + ubiquitin + E2 enzyme
- has-output: ubiquitylated E3 ligase
- occurs-in: eukaryotic cells
Key References:
- Buetow L., Huang D. T. (2021). International Journal of Molecular Sciences , 22, 6057.
- Nityanandam R. et al. (2011). BMC Biochemistry , 12, 33.
4. Autoregulation of Gene Expression (±)
A gene product regulates transcription of the same gene through positive or negative feedback, tuning gene expression dynamics, noise, and homeostasis.
Synonyms
self-regulation, autonomous regulation, homeostatic control
Antonyms
heteroregulation, external regulation
Related Terms
homeostasis, feedback control
Core Ontology Relations
- is-a: gene regulatory feedback motif
- part-of: transcriptional regulatory network
- regulates: mRNA abundance and response time
- has-input: gene product (protein or RNA)
- has-output: altered transcription rate
- occurs-in: bacteria, yeast, multicellular organisms
Key References:
- Alon U. (2007). Nature Reviews Genetics , 8, 450-461.
- Becskei A., Serrano L. (2000). Nature , 405, 590-593.
5. Autoinducer Molecules in Quorum Sensing (+)
Small diffusible molecules synthesized and detected by bacteria. Their accumulation with increasing cell density triggers coordinated community-wide transcriptional changes.
Synonyms
self-induction, auto-stimulation, positive feedback induction
Antonyms
autorepression, negative feedback
Related Terms
autoactivation, positive feedback
Core Ontology Relations
- is-a: extracellular signaling molecule
- part-of: quorum-sensing signal-response system
- regulates: group-level behavior and virulence
- has-input: bacterial metabolic pathways
- has-output: receptor activation and transcriptional changes
- occurs-in: bacterial populations
Key References:
- Papenfort K., Bassler B. L. (2016). Nature Reviews Microbiology , 14, 576-588.
- Mukherjee S., Bassler B. L. (2019). Nature Reviews Microbiology , 17, 371-382.
6. Autoinhibition within Proteins (–)
Intrinsic structural interactions prevent inappropriate activation of a protein, maintaining it in an inactive state until relieved by ligand binding, structural rearrangement, or post-translational modification.
Synonyms
self-inhibition, negative autoregulation, self-repression
Antonyms
autoactivation, positive autoregulation
Related Terms
negative feedback, autorepression
Core Ontology Relations
- is-a: intrinsic negative regulatory process
- part-of: protein activity control
- regulates: activation threshold and specificity
- has-input: inactive protein structure
- has-output: relieved inhibition and activation
- occurs-in: multi-domain signaling proteins
Key References:
- Fenton M. et al. (2023). Cell Reports , 42, 112739.
- Khan R. B. et al. (2019). Frontiers in Molecular Biosciences , 6, 144.
7. Autolysis (–)
Self-degradation mediated by endogenous lytic enzymes, occurring during programmed cell death, post-mortem breakdown, or engineered microbial lysis systems.
Synonyms
self-cleavage, autocatalytic cleavage, self-proteolysis
Antonyms
heterolysis, trans-cleavage
Related Terms
autocatalysis
Core Ontology Relations
- is-a: lytic cell death mechanism
- part-of: cellular degradation process
- regulates: release of intracellular contents
- has-input: endogenous hydrolases
- has-output: membrane rupture and component release
- occurs-in: microbes, tissues, postmortem environments
Key References:
- Yamaguchi Y., Nariya H., Inouye M. (2013). Applied and Environmental Microbiology , 79, 3120-3126.
- Pérez-Torrado R. et al. (2015). Comprehensive Reviews in Food Science and Food Safety , 14, 726-743.
SOORENA
Patch Notes
SOORENA
About SOORENA
Self-lOOp containing or autoREgulatory Nodes in biological network Analysis
SOORENA is a comprehensive database for exploring autoregulatory mechanisms in proteins. Our machine learning-powered platform analyzes millions of scientific publications to identify and classify autoregulatory protein mechanisms, providing researchers with unprecedented access to this critical biological information.
Project Contributors
Hala Arar
Department of Statistics
University of British Columbia
Vancouver, BC, Canada
Mohieddin Jafari
Department of Biochemistry and Developmental Biology
University of Helsinki, Finland
Faculty of Medicine and Health Technology, Tampere University, Finland
Tampere Institute for Advanced Study, Finland
Payman Nickchi
Department of Statistics
University of British Columbia
Vancouver, BC, Canada
Jehad Aldahdooh
Research Programs Unit
University of Helsinki
Helsinki, Finland
Acknowledgements
We would like to thank the following individuals for their valuable contributions to this project:
Zheng He • Yining Zhou • Mingyang Zhang