KO_pathway_ref

A comprehensive dataset mapping KEGG Orthology (KO) entries to metabolic pathways,
including module hierarchy, definitions, and enzyme annotations.

datasets

Provides tools for analyzing metabolic pathway completeness, abundance, and transcripts
using KEGG Orthology (KO) data from (meta)genomic and (meta)transcriptomic studies.
Supports both completeness (presence/absence) and abundance-weighted analyses.
Includes built-in KEGG reference datasets. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.

Liuyang Li

mclink

Metabolic Pathway Completeness and Abundance Calculation

KO_pathway_ref function

A data frame with 3846 rows (KO entries) and 10 variables:<dl>
<dt>Orthology_Entry</dt>
<dd>Character. KEGG Orthology ID (e.g., "K00844").</dd><dt>Module_Type</dt>
<dd>Character. Type of metabolic module (e.g., "Pathway modules").</dd><dt>Level_2</dt>
<dd>Character. Broad metabolic category (e.g., "Carbohydrate metabolism").</dd><dt>Level_3</dt>
<dd>Character. Specific metabolic subcategory (e.g., "Central carbohydrate metabolism").</dd><dt>Module_Entry</dt>
<dd>Character. KEGG Module ID (e.g., "M00001").</dd><dt>Module_Name</dt>
<dd>Character. Full name of the metabolic module (e.g., "Glycolysis (Embden-Meyerhof pathway), glucose =&gt; pyruvate").</dd><dt>Definition</dt>
<dd>Character. KO composition of the module, truncated in display (e.g., "(K00844,K12407,...)").</dd><dt>Orthology_Symbol</dt>
<dd>Character. Short symbol for the KO (e.g., "HK" for hexokinase).</dd><dt>Orthology_Name</dt>
<dd>Character. Full enzyme name with EC number (e.g., "hexokinase <code>[EC:2.7.1.1]</code>").</dd><dt>KO_Symbol</dt>
<dd>Character. Combined KO ID and symbol (e.g., "K00844; HK").</dd>
</dl>

Format

KEGG Orthology (KO) Pathway Information Dataset — KO_pathway_ref

A data frame with 3846 rows (KO entries) and 10 variables:<dl>
<dt>Orthology_Entry</dt>
<dd>Character. KEGG Orthology ID (e.g., "K00844").</dd>

<dt>Module_Type</dt>
<dd>Character. Type of metabolic module (e.g., "Pathway modules").</dd>

<dt>Level_2</dt>
<dd>Character. Broad metabolic category (e.g., "Carbohydrate metabolism").</dd>

<dt>Level_3</dt>
<dd>Character. Specific metabolic subcategory (e.g., "Central carbohydrate metabolism").</dd>

<dt>Module_Entry</dt>
<dd>Character. KEGG Module ID (e.g., "M00001").</dd>

<dt>Module_Name</dt>
<dd>Character. Full name of the metabolic module (e.g., "Glycolysis (Embden-Meyerhof pathway), glucose =&gt; pyruvate").</dd>

<dt>Definition</dt>
<dd>Character. KO composition of the module, truncated in display (e.g., "(K00844,K12407,...)").</dd>

<dt>Orthology_Symbol</dt>
<dd>Character. Short symbol for the KO (e.g., "HK" for hexokinase).</dd>

<dt>Orthology_Name</dt>
<dd>Character. Full enzyme name with EC number (e.g., "hexokinase <code>[EC:2.7.1.1]</code>").</dd>

<dt>KO_Symbol</dt>
<dd>Character. Combined KO ID and symbol (e.g., "K00844; HK").</dd>


</dl>

KO_pathway_ref: KEGG Orthology (KO) Pathway Information Dataset

Description

Usage

Arguments

Format