Skip to content

Class: GeneCluster

Ortholog cluster at species level. Clusters are classified as: - CORE: Present in all (or nearly all) genomes - AUXILIARY: Present in some genomes (shell genes) - SINGLETON: Present in only one genome (cloud genes)

SCALE: 132,531,501 gene clusters

PANGENOME STRUCTURE EXAMPLES: - K. pneumoniae: 4,199 core + 438,925 auxiliary = 443,124 total - S. aureus: 2,083 core + 145,831 auxiliary = 147,914 total

The core/auxiliary/singleton partition follows PPanGGOLiN methodology.

URI: https://w3id.org/kbase/kbase_ke_pangenome/GeneCluster

classDiagram class GeneCluster click GeneCluster href "../GeneCluster/" GeneCluster : gene_cluster_id GeneCluster : gtdb_species_clade_id GeneCluster --> "1" GtdbSpeciesClade : gtdb_species_clade_id click GtdbSpeciesClade href "../GtdbSpeciesClade/" GeneCluster : is_auxiliary GeneCluster : is_core GeneCluster : is_singleton GeneCluster : likelihood

Slots

Name Cardinality and Range Description Inheritance
gene_cluster_id 1
String		 Unique cluster identifier direct
gtdb_species_clade_id 1
GtdbSpeciesClade		 Species clade this cluster belongs to direct
is_core 0..1
Boolean		 Present in all (or nearly all) genomes direct
is_auxiliary 0..1
Boolean		 Present in some but not all genomes direct
is_singleton 0..1
Boolean		 Present in only one genome direct
likelihood 0..1
Float		 Log-likelihood from PPanGGOLiN Bayesian partitioning model direct

Usages

used by used in type used
GeneGeneclusterJunction gene_cluster_id range GeneCluster

Identifier and Mapping Information

Annotations

property value
source_table gene_cluster
row_count 132531501

Schema Source

  • from schema: https://w3id.org/kbase/kbase_ke_pangenome

Mappings

Mapping Type Mapped Value
self https://w3id.org/kbase/kbase_ke_pangenome/GeneCluster
native https://w3id.org/kbase/kbase_ke_pangenome/GeneCluster

LinkML Source

Direct

name: GeneCluster
annotations:
  source_table:
    tag: source_table
    value: gene_cluster
  row_count:
    tag: row_count
    value: '132531501'
description: 'Ortholog cluster at species level. Clusters are classified as: - CORE:
  Present in all (or nearly all) genomes - AUXILIARY: Present in some genomes (shell
  genes) - SINGLETON: Present in only one genome (cloud genes)

  SCALE: 132,531,501 gene clusters

  PANGENOME STRUCTURE EXAMPLES: - K. pneumoniae: 4,199 core + 438,925 auxiliary =
  443,124 total - S. aureus: 2,083 core + 145,831 auxiliary = 147,914 total

  The core/auxiliary/singleton partition follows PPanGGOLiN methodology.'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  gene_cluster_id:
    name: gene_cluster_id
    description: Unique cluster identifier. Often derived from seed gene ID.
    examples:
    - value: DXZZ01000056.1_1
    - value: NC_012808.1_2957
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    identifier: true
    domain_of:
    - GeneCluster
    - GeneGeneclusterJunction
    range: string
    required: true
  gtdb_species_clade_id:
    name: gtdb_species_clade_id
    description: Species clade this cluster belongs to
    comments:
    - 'Foreign key: GtdbSpeciesClade.gtdb_species_clade_id'
    examples:
    - value: s__Collinsella_sp902835305--GB_GCA_902835305.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    domain_of:
    - GtdbSpeciesClade
    - Genome
    - GeneCluster
    - Pangenome
    range: GtdbSpeciesClade
    required: true
  is_core:
    name: is_core
    description: Present in all (or nearly all) genomes. Core genes define species-level
      functions. Usually 10-20% of clusters.
    examples:
    - value: 'True'
      description: Essential housekeeping gene
    - value: 'False'
      description: Accessory gene
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GeneCluster
    range: boolean
  is_auxiliary:
    name: is_auxiliary
    description: Present in some but not all genomes. Shell/cloud genes. May include
      mobile elements, strain-specific adaptations.
    examples:
    - value: 'True'
    - value: 'False'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GeneCluster
    range: boolean
  is_singleton:
    name: is_singleton
    description: Present in only one genome. Often recently acquired genes, pseudogenes,
      or annotation artifacts. Usually 30-50% of clusters.
    examples:
    - value: 'True'
    - value: 'False'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GeneCluster
    range: boolean
  likelihood:
    name: likelihood
    description: Log-likelihood from PPanGGOLiN Bayesian partitioning model. More
      negative = stronger evidence for partition assignment.
    examples:
    - value: '-5.167393657456563'
    - value: '-2.5'
    - value: '-10.3'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    domain_of:
    - GeneCluster
    range: float

Induced

name: GeneCluster
annotations:
  source_table:
    tag: source_table
    value: gene_cluster
  row_count:
    tag: row_count
    value: '132531501'
description: 'Ortholog cluster at species level. Clusters are classified as: - CORE:
  Present in all (or nearly all) genomes - AUXILIARY: Present in some genomes (shell
  genes) - SINGLETON: Present in only one genome (cloud genes)

  SCALE: 132,531,501 gene clusters

  PANGENOME STRUCTURE EXAMPLES: - K. pneumoniae: 4,199 core + 438,925 auxiliary =
  443,124 total - S. aureus: 2,083 core + 145,831 auxiliary = 147,914 total

  The core/auxiliary/singleton partition follows PPanGGOLiN methodology.'
from_schema: https://w3id.org/kbase/kbase_ke_pangenome
attributes:
  gene_cluster_id:
    name: gene_cluster_id
    description: Unique cluster identifier. Often derived from seed gene ID.
    examples:
    - value: DXZZ01000056.1_1
    - value: NC_012808.1_2957
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    identifier: true
    alias: gene_cluster_id
    owner: GeneCluster
    domain_of:
    - GeneCluster
    - GeneGeneclusterJunction
    range: string
    required: true
  gtdb_species_clade_id:
    name: gtdb_species_clade_id
    description: Species clade this cluster belongs to
    comments:
    - 'Foreign key: GtdbSpeciesClade.gtdb_species_clade_id'
    examples:
    - value: s__Collinsella_sp902835305--GB_GCA_902835305.1
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    alias: gtdb_species_clade_id
    owner: GeneCluster
    domain_of:
    - GtdbSpeciesClade
    - Genome
    - GeneCluster
    - Pangenome
    range: GtdbSpeciesClade
    required: true
  is_core:
    name: is_core
    description: Present in all (or nearly all) genomes. Core genes define species-level
      functions. Usually 10-20% of clusters.
    examples:
    - value: 'True'
      description: Essential housekeeping gene
    - value: 'False'
      description: Accessory gene
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: is_core
    owner: GeneCluster
    domain_of:
    - GeneCluster
    range: boolean
  is_auxiliary:
    name: is_auxiliary
    description: Present in some but not all genomes. Shell/cloud genes. May include
      mobile elements, strain-specific adaptations.
    examples:
    - value: 'True'
    - value: 'False'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: is_auxiliary
    owner: GeneCluster
    domain_of:
    - GeneCluster
    range: boolean
  is_singleton:
    name: is_singleton
    description: Present in only one genome. Often recently acquired genes, pseudogenes,
      or annotation artifacts. Usually 30-50% of clusters.
    examples:
    - value: 'True'
    - value: 'False'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: is_singleton
    owner: GeneCluster
    domain_of:
    - GeneCluster
    range: boolean
  likelihood:
    name: likelihood
    description: Log-likelihood from PPanGGOLiN Bayesian partitioning model. More
      negative = stronger evidence for partition assignment.
    examples:
    - value: '-5.167393657456563'
    - value: '-2.5'
    - value: '-10.3'
    from_schema: https://w3id.org/kbase/kbase_ke_pangenome
    rank: 1000
    alias: likelihood
    owner: GeneCluster
    domain_of:
    - GeneCluster
    range: float