Use this guide to find one of the 158 LISA categories and understand the biological scope in which the fixed dictionary places it. The catalogue records dictionary assignments and representative member gene sets, not the enrichment result of a particular study.
In R or RStudio, read the installed catalogue as an ordinary data frame:
catalog_path <- system.file(
"extdata", "semantic-catalog", "semantic_category_catalog.tsv",
package = "lisaR", mustWork = TRUE
)
semantic_catalog <- read.delim(
catalog_path, sep = "\t", quote = "", comment.char = "",
colClasses = "character", check.names = FALSE
)
View(semantic_catalog)Filter by words in the display name or description when you do not yet know an ID:
query <- "repair|checkpoint"
matches <- grepl(
query,
paste(
semantic_catalog$category_display_name,
semantic_catalog$category_description
),
ignore.case = TRUE
)
semantic_catalog[matches, c(
"universe", "category_id", "category_display_name",
"macrogroup_name", "core_member_gene_sets"
)]Once you have an exact ID, select it together with its collection. This avoids matching a similar label in the wrong biological scope:
chosen <- semantic_catalog[
semantic_catalog$universe == "GOBP-C2" &
semantic_catalog$category_id == "DNA_DAMAGE_REPAIR_CHECKPOINTS",
c("category_display_name", "macrogroup_name", "core_member_gene_sets",
"example_gene_set_1", "example_gene_set_2", "example_gene_set_3")
]
stopifnot(nrow(chosen) == 1L)
print(chosen, row.names = FALSE)View() opens the data frame in RStudio’s viewer; the
other examples print subsets in the R console. The count is membership
in the core dictionary. The one to three examples illustrate the
category’s scope. They are not its full membership list or the strongest
results from your study. The report’s evidence sheet, not this
catalogue, supplies NES, FDR, leading edges and gene-level DE.
A gene set may be assigned to two categories in one supercategory. It then contributes one distinct set but two assignments. The bundled count table lets you check that distinction directly:
semantic_counts <- read.delim(system.file(
"extdata", "semantic-catalog", "semantic_supercategory_counts.tsv",
package = "lisaR", mustWork = TRUE
), sep = "\t", check.names = FALSE)
pi3k <- semantic_counts[
semantic_counts$macrogroup_id == "PI3K_AKT_MTOR",
c("universe", "macrogroup_id", "core_distinct_gene_sets",
"core_member_assignments")
]
stopifnot(nrow(pi3k) == 1L,
pi3k$core_distinct_gene_sets == 59L,
pi3k$core_member_assignments == 88L)
print(pi3k, row.names = FALSE)The 59 distinct gene sets have 88 assignments across categories in this supercategory. Assignment counts and distinct gene-set counts therefore measure different properties of the dictionary.
To open the corresponding study evidence, use the category navigator or gene search described in the report guide.
The four semantic collections are GOBP-C2,
GOMF, GOCC and PATHWAYS.
HALLMARKS is a separate direct gene-set collection, not
another LISA category catalogue. Category descriptions and one to three
exact member identifiers were checked against
lisa_dictionary_core@1.0.0. The existing provenance also
checks the same category vocabulary in
lisa_dictionary_expanded@1.0.0; this guide does not compare
tiers or study results.
The biological summary before each table describes the supercategory.
Within a table, read the exact category label and representative member
IDs together. The installed catalogue also includes a
category_description field for text searches. Its
descriptions restate the category labels.
Descriptions and examples delimit a theme; they do not assert activation, inhibition or causality. Example selection uses semantic representativeness and stable tie-breaking on specificity, lexical match and gene-set identifier. Dictionary membership supplies no numerical weight or gene-priority score. Study evidence uses the member gene sets’ enrichment and gene-level results.
Unassigned gene sets remain in the complete tested universe. The
OTHER_UNCLASSIFIED residual is tabular, not a biological
category or figure. For GOBP-C2, GOMF and
GOCC it has dedicated residual tables;
PATHWAYS retains the complete GSEA ledger without a
separate residual table.
The core and expanded classification dictionaries and category map
are included in lisaR. Gene-set-to-gene memberships are a separate
external resource. Source conditions are recorded in
THIRD_PARTY_NOTICES.md. See Resources and provenance for
those resource roles; no additional resource installation is needed to
read this catalogue.
Source versions and checksums accompany the installed catalogue in
extdata/semantic-catalog/SEMANTIC_CATALOG_PROVENANCE.tsv.
The active category map contains only categories with at least one exact assignment in the core or expanded dictionary. Supercategories without a retained category are absent from the active map.
| Collection | Supercategories | Categories | Core member assignments |
|---|---|---|---|
GOBP-C2 |
10 | 40 | 11729 |
GOMF |
9 | 37 | 1860 |
GOCC |
6 | 12 | 1003 |
PATHWAYS |
17 | 69 | 921 |
GOBP-C2Use this collection for biological processes and programmes. It combines Gene Ontology Biological Process with selected curated C2 pathway families, so one supercategory can span cellular mechanisms, tissues and organismal development. Read the exact member IDs before narrowing a broad category to one experimental mechanism.
DEVELOPMENT_NEURAL)Groups developmental, morphogenetic, neurogenic and synaptic biological programmes.
Verified membership: 2 categories, 1738 distinct core gene sets and 1801 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Development and morphogenesis
(DEVELOPMENT_MORPHOGENESIS) |
1010 | GOBP_DEVELOPMENTAL_GROWTH_INVOLVED_IN_MORPHOGENESISGOBP_EAR_DEVELOPMENTWP_HEART_DEVELOPMENT |
Neurogenesis and synapse (NEUROGENESIS_SYNAPSE) |
791 | GOBP_NEUROGENESISGOBP_REGULATION_OF_NEUROGENESISGOBP_SYNAPSE_PRUNING |
GENOME_GENE_EXPRESSION)Groups genome maintenance and the transcriptional, post-transcriptional and translational control of gene expression.
Verified membership: 4 categories, 1076 distinct core gene sets and 1090 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
DNA damage, repair and checkpoints
(DNA_DAMAGE_REPAIR_CHECKPOINTS) |
295 | GOBP_REGULATION_OF_DNA_DAMAGE_CHECKPOINTGOBP_DNA_REPAIRREACTOME_DNA_REPAIR |
RNA processing and RNP biology
(RNA_PROCESSING_SPLICING_RNP) |
263 | GOBP_RNA_PROCESSINGGOBP_MITOCHONDRIAL_RNA_PROCESSINGGOBP_RNA_3_END_PROCESSING |
Transcription, chromatin and epigenetics
(TRANSCRIPTION_CHROMATIN_EPIGENETICS) |
416 | GOBP_CHROMATIN_LOOPINGGOBP_MRNA_TRANSCRIPTIONGOBP_RRNA_TRANSCRIPTION |
Translation and ribosome (TRANSLATION_RIBOSOME) |
116 | KEGG_RIBOSOMEGOBP_TRANSLATIONREACTOME_TRANSLATION |
IMMUNE_INFLAMMATION)Groups adaptive, innate, cytokine, complement and antigen-presentation programmes in immune and inflammatory biology.
Verified membership: 4 categories, 1321 distinct core gene sets and 1356 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Adaptive immunity and antigen presentation
(IMMUNE_ADAPTIVE_ANTIGEN_MHC) |
328 | GOBP_ANTIGEN_PROCESSING_AND_PRESENTATIONKEGG_ANTIGEN_PROCESSING_AND_PRESENTATIONGOBP_REGULATION_OF_ANTIGEN_PROCESSING_AND_PRESENTATION |
Cytokine and inflammatory signaling
(IMMUNE_CYTOKINE_INFLAMMATORY) |
535 | WP_CYTOKINES_AND_INFLAMMATORY_RESPONSEBIOCARTA_INFLAM_PATHWAYBIOCARTA_CYTOKINE_PATHWAY |
Immune core (IMMUNE_CORE) |
185 | GOBP_REGULATION_OF_IMMUNE_RESPONSEGOBP_IMMUNE_EFFECTOR_PROCESSGOBP_ACTIVATION_OF_IMMUNE_RESPONSE |
Innate immunity, complement and PRR
(IMMUNE_INNATE_COMPLEMENT_PRR) |
308 | WP_COMPLEMENT_SYSTEMWP_COMPLEMENT_ACTIVATIONGOBP_COMPLEMENT_ACTIVATION |
METABOLISM_BIOENERGETICS)Groups amino-acid, carbohydrate, lipid, nucleotide, mitochondrial and detoxification programmes that support metabolism and energy balance.
Verified membership: 8 categories, 1560 distinct core gene sets and 1576 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Amino acid and one-carbon metabolism
(METABOLISM_AA_ONECARBON) |
251 | WP_AMINO_ACID_METABOLISMGOBP_AMINO_ACID_METABOLIC_PROCESSGOBP_ONE_CARBON_METABOLIC_PROCESS |
Carbohydrate metabolism and glycolysis
(METABOLISM_CARBOHYDRATE_GLYCOLYSIS) |
172 | GOBP_CARBOHYDRATE_METABOLIC_PROCESSGOBP_REGULATION_OF_CARBOHYDRATE_METABOLIC_PROCESSGOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS |
Detoxification and xenobiotic metabolism
(DETOX_XENOBIOTIC_METABOLISM) |
126 | GOBP_XENOBIOTIC_METABOLIC_PROCESSGOBP_DETOXIFICATIONREACTOME_XENOBIOTICS |
General metabolism (METABOLISM_CORE) |
51 | GOBP_ATP_METABOLIC_PROCESSGOBP_RECEPTOR_METABOLIC_PROCESSREACTOME_METABOLISM_OF_COFACTORS |
Lipid and fatty acid metabolism
(METABOLISM_LIPID_FA) |
637 | KEGG_FATTY_ACID_METABOLISMREACTOME_FATTY_ACID_METABOLISMGOBP_FATTY_ACID_METABOLIC_PROCESS |
Mitochondria, OXPHOS and ETC
(MITOCHONDRIA_OXPHOS_ETC) |
143 | BIOCARTA_ETC_PATHWAYGOBP_MITOCHONDRIAL_FUSIONGOBP_MITOCHONDRIAL_FISSION |
Nucleotide metabolism (METABOLISM_NUCLEOTIDE) |
175 | WP_NUCLEOTIDE_METABOLISMGOBP_NUCLEOBASE_METABOLIC_PROCESSGOBP_NUCLEOSIDE_METABOLIC_PROCESS |
Peroxisome and fatty acid oxidation
(PEROXISOME_FAO) |
21 | GOBP_FATTY_ACID_ALPHA_OXIDATIONKEGG_PEROXISOMEGOBP_FATTY_ACID_BETA_OXIDATION_USING_ACYL_COA_OXIDASE |
MICROENVIRONMENT_VASCULAR_ECM)Groups extracellular-matrix remodelling, vascular, angiogenic and lymphatic programmes in the tissue microenvironment.
Verified membership: 2 categories, 333 distinct core gene sets and 334 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
ECM and matrix remodeling (ECM_MATRIX_REMODELING) |
183 | REACTOME_ECM_PROTEOGLYCANSWP_MATRIX_METALLOPROTEINASESKEGG_ECM_RECEPTOR_INTERACTION |
Vascular, angiogenic and lymphatic biology
(VASCULAR_LYMPHATIC) |
151 | WP_ANGIOGENESISGOBP_VASCULOGENESISGOBP_REGULATION_OF_VASCULOGENESIS |
PROLIFERATION_CELL_CYCLE)Groups programmes governing DNA replication, mitosis and cell proliferation.
Verified membership: 1 category, 555 distinct core gene sets and 555 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Cell cycle and proliferation
(CELL_CYCLE_PROLIFERATION) |
555 | WP_CELL_CYCLEGOBP_CELL_CYCLEKEGG_CELL_CYCLE |
SIGNALING_COMMUNICATION)Groups broad growth-factor, hormonal and developmental pathways used for intercellular communication.
Verified membership: 5 categories, 1964 distinct core gene sets and 2015 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Core cell signaling (SIGNALING_CORE) |
714 | GOBP_CELL_CELL_SIGNALINGGOBP_CELL_ACTIVATIONGOBP_NEGATIVE_REGULATION_OF_CELL_COMMUNICATION |
Endocrine and hormonal pathways
(ENDOCRINE_HORMONAL) |
497 | GOBP_ENDOCRINE_HORMONE_SECRETIONGOBP_ENDOCRINE_PROCESSGOBP_REGULATION_OF_ENDOCRINE_PROCESS |
Growth factor and RTK pathways (GROWTH_FACTOR_RTK) |
412 | GOBP_RESPONSE_TO_GROWTH_FACTORGOBP_NERVE_GROWTH_FACTOR_SIGNALING_PATHWAYGOBP_GROWTH |
TGF-beta and SMAD signaling (TGFB_SMAD) |
129 | KEGG_TGF_BETA_SIGNALING_PATHWAYREACTOME_TGFBR3_REGULATES_TGF_BETA_SIGNALINGKEGG_MEDICUS_REFERENCE_TGF_BETA_SIGNALING_PATHWAY |
Wnt, Notch, Hedgehog and Hippo
(WNT_NOTCH_HEDGEHOG_HIPPO) |
263 | WNT_SIGNALINGWP_WNT_SIGNALINGPID_NOTCH_PATHWAY |
STRESS_DEATH_PROTEOSTASIS)Groups stress adaptation, autophagy, proteostasis and regulated cell-death programmes.
Verified membership: 7 categories, 879 distinct core gene sets and 901 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Apoptosis and regulated cell death
(APOPTOSIS_CELL_DEATH) |
321 | SA_PROGRAMMED_CELL_DEATHGOBP_PYROPTOTIC_CELL_DEATHGOBP_B_CELL_APOPTOTIC_PROCESS |
Autophagy, lysosome and phagosome maturation
(AUTOPHAGY_LYSOSOME) |
154 | GOBP_PHAGOSOME_MATURATIONGOBP_AUTOPHAGOSOME_MATURATIONGOBP_REGULATION_OF_AUTOPHAGOSOME_MATURATION |
ER stress and unfolded protein response
(ER_STRESS_UPR) |
48 | WP_UNFOLDED_PROTEIN_RESPONSEREACTOME_UNFOLDED_PROTEIN_RESPONSE_UPRGOBP_CELLULAR_RESPONSE_TO_UNFOLDED_PROTEIN |
Heat shock and acute stress response
(HEAT_SHOCK_STRESS_RESPONSE) |
17 | REACTOME_CELLULAR_RESPONSE_TO_HEAT_STRESSREACTOME_REGULATION_OF_HSF1_MEDIATED_HEAT_SHOCK_RESPONSE |
Hypoxia and HIF programs (HYPOXIA_HIF) |
31 | BIOCARTA_HIF_PATHWAYREACTOME_CELLULAR_RESPONSE_TO_HYPOXIAGOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_HYPOXIA |
Oxidative stress, redox and ROS
(OXIDATIVE_STRESS_REDOX_ROS) |
116 | WP_OXIDATIVE_STRESS_RESPONSEGOBP_RESPONSE_TO_OXIDATIVE_STRESSGOBP_REGULATION_OF_RESPONSE_TO_OXIDATIVE_STRESS |
Proteostasis, ubiquitin and proteasome
(PROTEOSTASIS_UBIQUITIN_PROTEASOME) |
214 | KEGG_UBIQUITIN_MEDIATED_PROTEOLYSISKEGG_PROTEASOMEGOBP_PROTEOLYSIS |
STRUCTURE_MOTILITY_PLASTICITY)Groups adhesion, polarity, cytoskeletal, migratory and cell-state-plasticity programmes.
Verified membership: 4 categories, 911 distinct core gene sets and 928 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Adhesion, junctions and polarity
(ADHESION_JUNCTION_POLARITY) |
260 | KEGG_GAP_JUNCTIONWP_FOCAL_ADHESIONGOBP_CELL_ADHESION |
Cytoskeleton and contractility
(CYTOSKELETON_CONTRACTILITY) |
419 | GOBP_MUSCLE_CONTRACTIONREACTOME_MUSCLE_CONTRACTIONGOBP_CYTOSKELETON_ORGANIZATION |
EMT and cell-state plasticity (EMT_PLASTICITY) |
34 | GOBP_MESENCHYMAL_CELL_MIGRATIONGOBP_MESENCHYMAL_CELL_DIFFERENTIATIONGOBP_NEURAL_CREST_CELL_DIFFERENTIATION |
Migration, invasion and motility programs
(MIGRATION_INVASION) |
215 | GOBP_CELL_MOTILITYGOBP_CELL_MIGRATIONGOBP_NEURON_MIGRATION |
TRANSPORT_TRAFFICKING_HOMEOSTASIS)Groups membrane transport, localisation, vesicle traffic and ionic homeostasis programmes.
Verified membership: 3 categories, 1150 distinct core gene sets and 1173 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Ion transport and homeostasis
(ION_TRANSPORT_HOMEOSTASIS) |
382 | REACTOME_ION_HOMEOSTASISGOBP_IRON_ION_TRANSPORTGOBP_ZINC_ION_TRANSPORT |
Transport and localization
(TRANSPORT_LOCALIZATION) |
418 | GOBP_REGULATION_OF_TRANSPORTGOBP_ADP_TRANSPORTGOBP_ATP_TRANSPORT |
Vesicle, endocytosis, exocytosis and secretion
(VESICLE_SECRETORY_TRAFFICKING) |
373 | GOBP_SYNAPTIC_VESICLE_EXOCYTOSISGOBP_ACROSOMAL_VESICLE_EXOCYTOSISGOBP_REGULATION_OF_SYNAPTIC_VESICLE_EXOCYTOSIS |
GOMFUse this collection for the molecular activity performed by a gene product, such as binding, catalysis, transport or receptor activity. It does not by itself say which broader biological process is active. Categories can overlap when one GO molecular-function set fits more than one functional grouping.
MF_CATALYTIC_METABOLIC)Groups molecular functions carried out by metabolic, redox, detoxification and other catalytic enzymes.
Verified membership: 7 categories, 358 distinct core gene sets and 368 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Amino-acid metabolic enzyme activity
(MF_AMINO_ACID_METAB) |
7 | GOMF_ACID_AMINO_ACID_LIGASE_ACTIVITYGOMF_L_AMINO_ACID_N_ACETYLTRANSFERASE_ACTIVITY |
Antioxidant and redox activity (MF_ANTIOX_REDOX) |
54 | GOMF_ANTIOXIDANT_ACTIVITYGOMF_PEROXIREDOXIN_ACTIVITYGOMF_THIOL_OXIDASE_ACTIVITY |
Carbohydrate metabolic enzyme activity
(MF_CARBOHYDRATE_METAB) |
58 | GOMF_CARBOHYDRATE_KINASE_ACTIVITYGOMF_CARBOHYDRATE_PHOSPHATASE_ACTIVITYGOMF_RACEMASE_AND_EPIMERASE_ACTIVITY_ACTING_ON_CARBOHYDRATES_AND_DERIVATIVES |
Detoxification and xenobiotic activity
(MF_DETOX_XENOBIOTIC) |
6 | GOMF_ARYL_SULFOTRANSFERASE_ACTIVITYGOMF_ESTROGEN_2_HYDROXYLASE_ACTIVITY |
General catalytic activity (MF_CATALYTIC) |
134 | GOMF_CATALYTIC_ACTIVITY_ACTING_ON_DNAGOMF_CATALYTIC_ACTIVITY_ACTING_ON_RNAGOMF_CATALYTIC_ACTIVITY_ACTING_ON_A_RRNA |
General metabolic enzyme activity
(MF_METABOLIC_ENZ) |
23 | GOMF_COA_TRANSFERASE_ACTIVITYGOMF_SULFOTRANSFERASE_ACTIVITYGOMF_SULFURTRANSFERASE_ACTIVITY |
Lipid metabolic enzyme activity (MF_LIPID_METAB) |
86 | GOMF_LIPASE_ACTIVITYGOMF_DEACYLASE_ACTIVITYGOMF_COA_LIGASE_ACTIVITY |
MF_CELL_CYCLE_DEVELOPMENT)Groups molecular regulators of cell-cycle progression, differentiation and developmental decisions.
Verified membership: 2 categories, 4 distinct core gene sets and 4 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Cell-cycle regulatory activity (MF_CELL_CYCLE_REG) |
3 | GOMF_CYCLIN_DEPENDENT_PROTEIN_KINASE_REGULATOR_ACTIVITY |
Developmental regulator activity
(MF_DEVELOPMENT_REG) |
1 | GOMF_MORPHOGEN_ACTIVITY |
MF_GENE_EXPRESSION)Groups chromatin, transcription, RNA-processing and translation-related molecular functions.
Verified membership: 4 categories, 170 distinct core gene sets and 170 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Epigenetic and chromatin activity (MF_EPIGENETIC) |
73 | GOMF_CHROMATIN_DNA_BINDINGGOMF_CHROMATIN_PROTEIN_ADAPTOR_ACTIVITYGOMF_PROMOTER_SPECIFIC_CHROMATIN_BINDING |
RNA processing activity (MF_RNA_PROCESSING) |
47 | GOMF_RNA_NUCLEASE_ACTIVITYGOMF_RNA_POLYMERASE_ACTIVITYGOMF_RNA_EXONUCLEASE_ACTIVITY |
Transcription regulation activity
(MF_TRANSCRIPTION_REG) |
41 | GOMF_TRANSCRIPTION_REGULATOR_ACTIVITYGOMF_TRANSCRIPTION_COACTIVATOR_ACTIVITYGOMF_TRANSCRIPTION_COREGULATOR_ACTIVITY |
Translation regulation activity
(MF_TRANSLATION_REG) |
9 | GOMF_TRANSLATION_FACTOR_ACTIVITYGOMF_TRANSLATION_ACTIVATOR_ACTIVITY |
MF_GENERIC_OTHER)Groups broad binding or host-interaction molecular functions that do not fit a more specific functional class.
Verified membership: 2 categories, 525 distinct core gene sets and 526 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Binding activity (MF_BINDING) |
525 | GOMF_ADP_BINDINGGOMF_AMP_BINDINGGOMF_BMP_BINDING |
Viral-host molecular function (MF_VIRAL_HOST) |
1 | GOMF_VIRION_BINDING |
MF_IMMUNE_LIGAND_RECEPTOR)Groups immune recognition, complement, receptor and extracellular ligand molecular functions.
Verified membership: 3 categories, 53 distinct core gene sets and 53 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Complement molecular function (MF_COMPLEMENT) |
3 | GOMF_COMPLEMENT_BINDING |
Cytokine, chemokine, growth-factor and hormone ligand activity
(MF_CYTOKINE_GROWTH) |
12 | GOMF_GROWTH_FACTOR_ACTIVITYGOMF_HORMONE_ACTIVITY |
Immune receptor and antigen-recognition activity
(MF_IMMUNE_RECEPTOR) |
38 | GOMF_IMMUNE_RECEPTOR_ACTIVITYGOMF_PATTERN_RECOGNITION_RECEPTOR_ACTIVITYGOMF_PEPTIDOGLYCAN_IMMUNE_RECEPTOR_ACTIVITY |
MF_PROTEOSTASIS_STRESS_DEATH)Groups molecular functions involved in proteostasis, stress responses, proteolysis and regulated cell death.
Verified membership: 5 categories, 82 distinct core gene sets and 84 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Apoptosis and cell-death regulatory activity
(MF_APOPTOSIS_REG) |
3 | GOMF_DEATH_RECEPTOR_ACTIVITY |
Protease and protease inhibitor activity
(MF_PROTEASE_INHIB) |
40 | GOMF_PEPTIDASE_INHIBITOR_ACTIVITYGOMF_METALLOENDOPEPTIDASE_INHIBITOR_ACTIVITYGOMF_MOLECULAR_FUNCTION_INHIBITOR_ACTIVITY |
Protein folding and degradation activity
(MF_PROTEIN_FOLDING_DEG) |
11 | GOMF_PROTEIN_FOLDING_CHAPERONEGOMF_PROTEIN_FOLDING_CHAPERONE_BINDING |
Stress-response molecular activity
(MF_STRESS_RESPONSE) |
2 | GOMF_HEAT_SHOCK_PROTEIN_BINDING |
Ubiquitin and SUMO ligase activity
(MF_LIGASE_SUMOYL) |
28 | GOMF_SUMO_LIGASE_ACTIVITYGOMF_UBIQUITIN_UBIQUITIN_LIGASE_ACTIVITYGOMF_HISTONE_UBIQUITIN_LIGASE_ACTIVITY |
MF_SIGNALING_REGULATION)Groups receptors, kinases, phosphatases, adaptors and enzyme regulators that control signalling.
Verified membership: 5 categories, 306 distinct core gene sets and 313 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Enzyme regulator activity (MF_ENZYME_REG) |
59 | GOMF_ENZYME_REGULATOR_ACTIVITYGOMF_ATPASE_REGULATOR_ACTIVITYGOMF_ENZYME_ACTIVATOR_ACTIVITY |
Intracellular signaling activity (MF_SIGNALING) |
12 | GOMF_GTPASE_ACTIVITYGOMF_G_PROTEIN_ACTIVITY |
Kinase and phosphatase activity
(MF_KINASE_PHOSPHATASE) |
104 | GOMF_PHOSPHATIDYLINOSITOL_KINASE_ACTIVITYGOMF_MAP_KINASE_PHOSPHATASE_ACTIVITYGOMF_INOSITOL_PHOSPHATE_KINASE_ACTIVITY |
Receptor activity (MF_RECEPTOR) |
122 | GOMF_BMP_RECEPTOR_ACTIVITYGOMF_WNT_RECEPTOR_ACTIVITYGOMF_GABA_RECEPTOR_ACTIVITY |
Scaffold and adaptor activity
(MF_SCAFFOLD_ADAPTER) |
16 | GOMF_SIGNALING_ADAPTOR_ACTIVITYGOMF_CARGO_ADAPTOR_ACTIVITY |
MF_STRUCTURE_ADHESION_ECM)Groups structural, motor, adhesion and extracellular-matrix molecular functions.
Verified membership: 4 categories, 54 distinct core gene sets and 55 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Adhesion molecular function (MF_ADHESION) |
12 | GOMF_CELL_ADHESION_MOLECULE_BINDINGGOMF_CELL_ADHESION_MEDIATOR_ACTIVITY |
Cytoskeleton and motor activity
(MF_CYTOSKELETON_MOTOR) |
13 | GOMF_CYTOSKELETAL_MOTOR_ACTIVITYGOMF_MICROTUBULE_MOTOR_ACTIVITY |
Extracellular matrix molecular function
(MF_EXTRACELL_MATRIX) |
13 | GOMF_EXTRACELLULAR_MATRIX_BINDINGGOMF_EXTRACELLULAR_MATRIX_PROTEIN_BINDING |
Structural constituent activity
(MF_STRUCTURAL_CONSTITUENT) |
17 | GOMF_STRUCTURAL_CONSTITUENT_OF_MUSCLEGOMF_STRUCTURAL_CONSTITUENT_OF_SYNAPSE |
MF_TRANSPORT_SENSING)Groups channels, pumps, transporters, vesicle-trafficking factors and physicochemical sensors.
Verified membership: 5 categories, 285 distinct core gene sets and 287 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Ion and physicochemical sensing activity
(MF_ION_SENSING) |
4 | GOMF_METAL_ION_SENSOR_ACTIVITY |
Ion channel and pump activity
(MF_ION_CHANNEL_PUMP) |
86 | GOMF_ATP_GATED_ION_CHANNEL_ACTIVITYGOMF_POTASSIUM_ION_LEAK_CHANNEL_ACTIVITYGOMF_MONOATOMIC_ION_GATED_CHANNEL_ACTIVITY |
Olfactory and taste receptor activity
(MF_OLFACTORY) |
6 | GOMF_TASTE_RECEPTOR_ACTIVITYGOMF_OLFACTORY_RECEPTOR_ACTIVITY |
Transporter activity (MF_TRANSPORTER) |
188 | GOMF_TRANSPORTER_ACTIVITYGOMF_LIPID_TRANSPORTER_ACTIVITYGOMF_PROTEIN_TRANSPORTER_ACTIVITY |
Vesicle trafficking activity (MF_VESICLE_TRAFFIC) |
3 | GOMF_SNARE_BINDING |
GOCCUse this collection for cellular locations, structures and complexes. A GOCC category can support a compartment-level interpretation, but enrichment is not direct evidence that a protein moved to that compartment or that the structure changed in abundance.
CC_SURFACE_ADHESION_ECM)Covers plasma-membrane, cell-junction, cytoskeletal and extracellular-matrix compartments.
Verified membership: 3 categories, 343 distinct core gene sets and 348 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Extracellular matrix compartment
(CC_EXTRACELLULAR_MATRIX) |
24 | GOCC_SPECIALIZED_EXTRACELLULAR_MATRIXGOCC_SYNAPSE_ASSOCIATED_EXTRACELLULAR_MATRIXGOCC_INTERSTITIAL_MATRIX |
Junction, adhesion and cytoskeletal compartment
(CC_JUNCTION_ADHESION_CYTOSKELETON) |
209 | GOCC_GAP_JUNCTIONGOCC_TIGHT_JUNCTIONGOCC_ADHERENS_JUNCTION |
Plasma membrane and cell-surface compartment
(CC_PLASMA_MEMBRANE_CELL_SURFACE) |
115 | GOCC_CELL_SURFACEGOCC_CELL_BODY_MEMBRANEGOCC_PLASMA_MEMBRANE_RAFT |
CC_IMMUNE_COMPLEXES)Covers cellular complexes that assemble immune and inflammatory signalling machinery.
Verified membership: 1 category, 29 distinct core gene sets and 29 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Immune signaling and inflammatory complex compartment
(CC_IMMUNE_SIGNALING_COMPLEX) |
29 | GOCC_NLRP1_INFLAMMASOME_COMPLEXGOCC_NLRP3_INFLAMMASOME_COMPLEXGOCC_CANONICAL_INFLAMMASOME_COMPLEX |
CC_METABOLIC_ORGANELLES)Covers organelles that host energy production and intermediary metabolism, especially mitochondria and peroxisomes.
Verified membership: 1 category, 46 distinct core gene sets and 46 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Mitochondrial and metabolic organelle compartment
(CC_MITOCHONDRIAL_METABOLIC) |
46 | GOCC_MITOCHONDRIONGOCC_ORGANELLAR_RIBOSOMEGOCC_MITOCHONDRIAL_CRISTA |
CC_NUCLEAR_GENE_EXPRESSION)Covers nuclear, chromatin, transcriptional, RNA-processing and ribosomal compartments.
Verified membership: 2 categories, 275 distinct core gene sets and 277 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Nuclear and chromatin compartment
(CC_NUCLEAR_CHROMATIN) |
137 | GOCC_CHROMATINGOCC_NUCLEAR_BODYGOCC_NUCLEAR_PORE |
Transcription, RNA and ribosome complexes
(CC_TRANSCRIPTION_RNA_RIBOSOME) |
140 | GOCC_RNA_DECAPPING_COMPLEXGOCC_RNA_POLYMERASE_COMPLEXGOCC_TRANSCRIPTION_EXPORT_COMPLEX |
CC_PROTEOSTASIS_GENERIC_COMPLEXES)Covers macromolecular complexes involved in protein folding, degradation and other general protein assemblies.
Verified membership: 2 categories, 76 distinct core gene sets and 76 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Other generic protein/macromolecular complex
(CC_OTHER_GENERIC_COMPLEX) |
42 | GOCC_PROTEIN_KINASE_COMPLEXGOCC_MEMBRANE_PROTEIN_COMPLEXGOCC_PROTEIN_PHOSPHATASE_4_COMPLEX |
Proteostasis complex compartment
(CC_PROTEOSTASIS_COMPLEX) |
34 | GOCC_3M_COMPLEXGOCC_RQC_COMPLEXGOCC_PREFOLDIN_COMPLEX |
CC_SECRETORY_ENDOMEMBRANE)Covers endoplasmic-reticulum, Golgi, vesicular, endolysosomal and secretory compartments.
Verified membership: 3 categories, 226 distinct core gene sets and 227 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Endolysosome, autophagy and intracellular vesicle compartment
(CC_ENDOLYSOSOME_AUTOPHAGY_VESICLE) |
116 | GOCC_ENDOLYSOSOMEGOCC_AUTOPHAGOSOMEGOCC_VESICLE_COAT |
ER, Golgi and secretory-route compartment
(CC_ER_GOLGI_SECRETORY) |
96 | GOCC_ENDOPLASMIC_RETICULUM_GOLGI_INTERMEDIATE_COMPARTMENTGOCC_GOLGI_LUMENGOCC_GOLGI_STACK |
Extracellular vesicle and secretome compartment
(CC_EXTRACELLULAR_VESICLE_SECRETOME) |
15 | GOCC_CHYLOMICRONGOCC_MICROVESICLE |
PATHWAYSUse this stricter signalling collection to distinguish named receptors, branches and downstream cascades within the broader GOBP-C2 space. Categories can share a gene set when a curated pathway crosses more than one branch. A category label organises the saved enrichment evidence; it is not a claim that the named pathway is activated.
RTK_RAS_MAPK)Groups receptor-tyrosine-kinase signalling through RAS and the RAF-MEK-ERK cascade.
Verified membership: 12 categories, 252 distinct core gene sets and 279 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
EGFR/ERBB signaling (EGFR_ERBB_SIGNALING) |
67 | WP_ERBB_SIGNALINGGOBP_ERBB_SIGNALING_PATHWAYKEGG_ERBB_SIGNALING_PATHWAY |
FGFR signaling (FGFR_SIGNALING) |
42 | REACTOME_SIGNALING_BY_FGFRKEGG_MEDICUS_REFERENCE_FGF_FGFR_PI3K_SIGNALING_PATHWAYKEGG_MEDICUS_REFERENCE_FGF_FGFR_RAS_ERK_SIGNALING_PATHWAY |
VEGF/VEGFR signaling (VEGF_VEGFR_SIGNALING) |
11 | PID_VEGF_VEGFR_PATHWAYBIOCARTA_VEGF_PATHWAY |
PDGF/PDGFR signaling (PDGF_PDGFRA_B_SIGNALING) |
15 | WP_PDGF_PATHWAYBIOCARTA_PDGF_PATHWAY |
MET/HGF signaling (MET_HGF_SIGNALING) |
15 | PID_MET_PATHWAYBIOCARTA_MET_PATHWAY |
KIT signaling (KIT_SIGNALING) |
8 | PID_KIT_PATHWAYWP_KIT_RECEPTOR_SIGNALING |
RET signaling (RET_SIGNALING) |
6 | PID_RET_PATHWAYREACTOME_RET_SIGNALING |
Insulin/IGF signaling (INSULIN_IGF_SIGNALING) |
25 | PID_INSULIN_PATHWAYWP_INSULIN_SIGNALINGBIOCARTA_INSULIN_PATHWAY |
RAS activation (RAS_ACTIVATION) |
16 | PID_RAS_PATHWAYWP_RAS_SIGNALING |
RAF-MEK-ERK cascade (RAF_MEK_ERK_CASCADE) |
43 | BIOCARTA_ERK_PATHWAYWP_MAPK_CASCADEREACTOME_RAF_ACTIVATION |
ALK signaling (ALK_SIGNALING) |
7 | BIOCARTA_ALK_PATHWAYREACTOME_SIGNALING_BY_ALK |
NTRK/TRK signaling (NTRK_TRK_SIGNALING) |
24 | PID_MAPK_TRK_PATHWAYPID_PI3K_PLC_TRK_PATHWAYGOBP_NEUROTROPHIN_TRK_RECEPTOR_SIGNALING_PATHWAY |
STRESS_MAPK)Groups stress-responsive p38 and JNK mitogen-activated protein kinase pathways.
Verified membership: 2 categories, 21 distinct core gene sets and 21 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
p38 MAPK signaling (P38_MAPK_SIGNALING) |
12 | WP_P38_MAPK_SIGNALINGPID_P38_MK2_PATHWAY |
JNK signaling (JNK_SIGNALING) |
9 | GOBP_JNK_CASCADEKEGG_MEDICUS_REFERENCE_FAS_JNK_SIGNALING_PATHWAY |
PI3K_AKT_MTOR)Groups PI3K, AKT, mTOR and AMPK pathways that coordinate growth, survival and nutrient sensing.
Verified membership: 5 categories, 59 distinct core gene sets and 88 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Class I PI3K signaling (PI3K_CLASS_I_SIGNALING) |
33 | REACTOME_PI3K_AKT_ACTIVATIONKEGG_MEDICUS_REFERENCE_P4_PR_PI3K_SIGNALING_PATHWAYKEGG_MEDICUS_REFERENCE_HGF_MET_PI3K_SIGNALING_PATHWAY |
AKT signaling (AKT_SIGNALING) |
37 | BIOCARTA_AKT_PATHWAYPID_PI3KCI_AKT_PATHWAYREACTOME_PI3K_AKT_ACTIVATION |
mTORC1 signaling (MTORC1_SIGNALING) |
11 | REACTOME_MTORC1_MEDIATED_SIGNALLINGREACTOME_AMINO_ACIDS_REGULATE_MTORC1 |
mTORC2 signaling (MTORC2_SIGNALING) |
1 | GOBP_TORC2_SIGNALING |
AMPK signaling (AMPK_SIGNALING) |
6 | GOBP_CAMKK_AMPK_SIGNALING_CASCADEREACTOME_ACTIVATION_OF_AMPK_DOWNSTREAM_OF_NMDARS |
RHO_GTPASE_CYTOSKELETON)Groups RHO-family GTPase, adhesion and actin-regulatory pathways that organise cell shape and movement.
Verified membership: 6 categories, 33 distinct core gene sets and 37 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
RAC1 signaling (RAC1_SIGNALING) |
10 | PID_RAC1_PATHWAYBIOCARTA_RAC1_PATHWAY |
RHOA-ROCK signaling (RHOA_ROCK_SIGNALING) |
11 | PID_RHOA_PATHWAYREACTOME_RHOA_GTPASE_CYCLE |
CDC42 signaling (CDC42_SIGNALING) |
8 | PID_CDC42_PATHWAYPID_CDC42_REG_PATHWAY |
PAK signaling (PAK_SIGNALING) |
2 | KEGG_MEDICUS_REFERENCE_RAC_CDC42_PAK_ERK_SIGNALING_PATHWAY |
FAK/SRC adhesion signaling (FAK_SRC_SIGNALING) |
5 | PID_FAK_PATHWAY |
Actin regulatory signaling
(ACTIN_REGULATORY_SIGNALING) |
1 | REACTOME_RHO_GTPASES_ACTIVATE_WASPS_AND_WAVES |
TGF_BETA_SMAD)Groups TGF-beta-family ligands and their SMAD-dependent developmental and homeostatic pathways.
Verified membership: 3 categories, 31 distinct core gene sets and 31 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
TGF-beta/SMAD signaling (TGF_BETA_SMAD_SIGNALING) |
17 | KEGG_TGF_BETA_SIGNALING_PATHWAYREACTOME_TGFBR3_REGULATES_TGF_BETA_SIGNALING |
BMP/SMAD signaling (BMP_SMAD_SIGNALING) |
8 | PID_BMP_PATHWAYREACTOME_SIGNALING_BY_BMP |
Activin/Nodal signaling (ACTIVIN_NODAL_SIGNALING) |
6 | GOBP_NODAL_SIGNALING_PATHWAYREACTOME_SIGNALING_BY_NODAL |
WNT_NOTCH_HEDGEHOG)Groups WNT, NOTCH and Hedgehog developmental signalling, including canonical and non-canonical branches.
Verified membership: 4 categories, 94 distinct core gene sets and 94 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
WNT/beta-catenin signaling
(WNT_BETA_CATENIN_SIGNALING) |
37 | WNT_SIGNALINGPID_BETA_CATENIN_DEG_PATHWAYPID_BETA_CATENIN_NUC_PATHWAY |
Non-canonical WNT/PCP signaling
(NONCANONICAL_WNT_PCP_SIGNALING) |
6 | GOBP_NON_CANONICAL_WNT_SIGNALING_PATHWAYREACTOME_PCP_CE_PATHWAY |
NOTCH signaling (NOTCH_SIGNALING) |
34 | PID_NOTCH_PATHWAYBIOCARTA_NOTCH_PATHWAYGOBP_NOTCH_SIGNALING_PATHWAY |
Hedgehog signaling (HEDGEHOG_SIGNALING) |
17 | KEGG_HEDGEHOG_SIGNALING_PATHWAYPID_HEDGEHOG_2PATHWAY |
HIPPO_MECHANOSIGNALING)Groups Hippo/YAP/TAZ and mechanotransduction pathways that connect tissue mechanics to cell-state regulation.
Verified membership: 2 categories, 7 distinct core gene sets and 8 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Hippo/YAP/TAZ signaling (HIPPO_YAP_TAZ_SIGNALING) |
7 | GOBP_HIPPO_SIGNALINGWP_HIPPO_SIGNALING_REGULATION |
Mechanotransduction signaling
(MECHANOTRANSDUCTION_SIGNALING) |
1 | WP_MECHANOREGULATION_AND_PATHOLOGY_OF_YAPTAZ_VIA_HIPPO_AND_NONHIPPO_MECHANISMS |
CYTOKINE_JAK_STAT)Groups cytokine pathways that transmit signals through JAK kinases and STAT transcription factors.
Verified membership: 6 categories, 52 distinct core gene sets and 52 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Type I interferon signaling
(TYPE_I_INTERFERON_SIGNALING) |
10 | WP_INTERFERON_TYPE_I_SIGNALINGGOBP_TYPE_I_INTERFERON_MEDIATED_SIGNALING_PATHWAY |
Type II interferon signaling
(TYPE_II_INTERFERON_SIGNALING) |
6 | WP_TYPE_II_INTERFERON_SIGNALINGGOBP_TYPE_II_INTERFERON_MEDIATED_SIGNALING_PATHWAY |
IL6/JAK/STAT3 signaling (IL6_JAK_STAT3_SIGNALING) |
9 | WP_IL6_SIGNALINGBIOCARTA_IL6_PATHWAY |
IL2/STAT5 signaling (IL2_STAT5_SIGNALING) |
11 | PID_IL2_STAT5_PATHWAYWP_IL2_SIGNALING |
IL10/STAT3 signaling (IL10_STAT3_SIGNALING) |
5 | BIOCARTA_IL10_PATHWAY |
IL12/IL23 signaling (IL12_IL23_STAT4_3_SIGNALING) |
11 | PID_IL23_PATHWAYBIOCARTA_IL12_PATHWAY |
INFLAMMATORY_NFKB)Groups canonical and non-canonical NF-kB pathways downstream of inflammatory receptors.
Verified membership: 4 categories, 54 distinct core gene sets and 55 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
TNF/NF-kB signaling (TNF_NFKB_SIGNALING) |
17 | PID_TNF_PATHWAYREACTOME_TNF_SIGNALING |
IL1/TLR-NF-kB signaling (IL1_TLR_NFKB_SIGNALING) |
17 | PID_IL1_PATHWAYWP_IL1_SIGNALING |
Canonical NF-kB signaling
(CANONICAL_NFKB_SIGNALING) |
15 | REACTOME_TRAF6_MEDIATED_NF_KB_ACTIVATIONGOBP_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION |
Non-canonical NF-kB signaling
(NONCANONICAL_NFKB_SIGNALING) |
6 | REACTOME_TNFR2_NON_CANONICAL_NF_KB_PATHWAYGOBP_NON_CANONICAL_NF_KAPPAB_SIGNAL_TRANSDUCTION |
INNATE_IMMUNE_SIGNALING)Groups pattern-recognition, nucleic-acid sensing and inflammasome pathways of innate immunity.
Verified membership: 4 categories, 54 distinct core gene sets and 54 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
TLR signaling (TLR_SIGNALING) |
30 | BIOCARTA_TOLL_PATHWAYGOBP_TOLL_SIGNALING_PATHWAYPID_TOLL_ENDOGENOUS_PATHWAY |
RIG-I/MDA5 signaling (RIG_I_MDA5_SIGNALING) |
9 | GOBP_RIG_I_SIGNALING_PATHWAYKEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY |
cGAS-STING signaling (CGAS_STING_SIGNALING) |
7 | GOBP_CGAS_STING_SIGNALING_PATHWAYKEGG_MEDICUS_REFERENCE_CGAS_STING_SIGNALING_PATHWAY |
NLRP3 inflammasome signaling
(NLRP3_INFLAMMASOME_SIGNALING) |
8 | REACTOME_THE_NLRP3_INFLAMMASOMEREACTOME_INFLAMMASOMES |
GPCR_SECOND_MESSENGER)Groups GPCR and phospholipase pathways that use cyclic nucleotides, calcium and other second messengers.
Verified membership: 5 categories, 64 distinct core gene sets and 69 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
GPCR-cAMP-PKA signaling (GPCR_CAMP_PKA_SIGNALING) |
31 | BIOCARTA_GPCR_PATHWAYGOBP_CAMP_PKA_SIGNAL_TRANSDUCTIONKEGG_MEDICUS_REFERENCE_PKA_HOLOENZYME |
GPCR-PLC-calcium signaling
(GPCR_PLC_CALCIUM_SIGNALING) |
16 | BIOCARTA_GPCR_PATHWAYKEGG_MEDICUS_REFERENCE_GPCR_PLCB_ITPR_SIGNALING_PATHWAY |
PLC-gamma signaling (PLC_GAMMA_SIGNALING) |
2 | KEGG_MEDICUS_REFERENCE_TCR_PLCG_ITPR_SIGNALING_PATHWAY |
Calcium/calcineurin/NFAT signaling
(CALCIUM_CALMODULIN_CALCINEURIN) |
12 | REACTOME_CALCINEURIN_ACTIVATES_NFATBIOCARTA_NFAT_PATHWAY |
S1P/EDG receptor signaling (S1P_EDG_SIGNALING) |
8 | WP_S1P_RECEPTOR_SIGNAL_TRANSDUCTIONPID_S1P_META_PATHWAY |
T_CELL_B_CELL_RECEPTOR_SIGNALING)Groups antigen-receptor and costimulatory signalling in T and B lymphocytes.
Verified membership: 3 categories, 36 distinct core gene sets and 37 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
T-cell receptor signaling (TCR_SIGNALING) |
17 | GOBP_T_CELL_RECEPTOR_SIGNALING_PATHWAYKEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY |
B-cell receptor signaling (BCR_SIGNALING) |
13 | WP_B_CELL_RECEPTOR_SIGNALINGGOBP_B_CELL_RECEPTOR_SIGNALING_PATHWAY |
CD28 costimulation signaling
(CD28_COSTIMULATION_SIGNALING) |
7 | REACTOME_CD28_DEPENDENT_VAV1_PATHWAYREACTOME_CO_STIMULATION_BY_CD28 |
DEATH_RECEPTOR_SIGNALING)Groups extrinsic cell-death pathways initiated by death receptors and their proximal signalling complexes.
Verified membership: 2 categories, 14 distinct core gene sets and 16 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
FAS/death receptor signaling
(FAS_DEATH_RECEPTOR_SIGNALING) |
10 | REACTOME_DEATH_RECEPTOR_SIGNALINGPID_FAS_PATHWAY |
TRAIL death receptor signaling
(TRAIL_DEATH_RECEPTOR_SIGNALING) |
6 | REACTOME_DEATH_RECEPTOR_SIGNALINGPID_TRAIL_PATHWAY |
NUCLEAR_RECEPTOR_SIGNALING)Groups signalling and transcriptional programmes controlled by steroid and metabolic nuclear receptors.
Verified membership: 3 categories, 22 distinct core gene sets and 22 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Estrogen receptor signaling
(ESTROGEN_RECEPTOR_SIGNALING) |
9 | WP_ESTROGEN_RECEPTOR_PATHWAYGOBP_ESTROGEN_RECEPTOR_SIGNALING_PATHWAY |
Androgen receptor signaling
(ANDROGEN_RECEPTOR_SIGNALING) |
5 | WP_ANDROGEN_RECEPTOR_SIGNALING |
PPAR signaling (PPAR_SIGNALING) |
8 | WP_PPAR_SIGNALINGKEGG_PPAR_SIGNALING_PATHWAY |
STRESS_RESPONSE_SIGNALING)Groups NRF2 antioxidant and unfolded-protein-response branches that manage oxidative and endoplasmic-reticulum stress.
Verified membership: 4 categories, 24 distinct core gene sets and 26 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
NRF2/KEAP1 signaling (NRF2_KEAP1_SIGNALING) |
11 | WP_NRF2_PATHWAYKEGG_MEDICUS_REFERENCE_KEAP1_NRF2_SIGNALING_PATHWAY |
PERK/ATF4 UPR signaling (UPR_PERK_ATF4_SIGNALING) |
8 | KEGG_MEDICUS_VARIANT_SCRAPIE_CONFORMATION_PRPSC_TO_PERK_ATF4_SIGNALING_PATHWAYKEGG_MEDICUS_VARIANT_MUTATION_CAUSED_ABERRANT_SNCA_TO_PERK_ATF4_SIGNALING_PATHWAY |
IRE1/XBP1 UPR signaling (IRE1_XBP1_SIGNALING) |
3 | GOBP_IRE1_MEDIATED_UNFOLDED_PROTEIN_RESPONSE |
ATF6 UPR signaling (ATF6_UPR_SIGNALING) |
4 | GOBP_ATF6_MEDIATED_UNFOLDED_PROTEIN_RESPONSE |
RTK_MATRIX_GUIDANCE_SIGNALING)Groups receptor and guidance pathways that connect extracellular cues, matrix interactions and directed cell behaviour.
Verified membership: 3 categories, 20 distinct core gene sets and 20 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
Ephrin/EPH signaling (EPHRIN_EPH_SIGNALING) |
11 | REACTOME_EPH_EPHRIN_SIGNALINGREACTOME_EPHRIN_SIGNALING |
DDR1/DDR2 collagen receptor signaling
(DDR1_DDR2_COLLAGEN_RECEPTOR_SIGNALING) |
1 | GOBP_COLLAGEN_ACTIVATED_TYROSINE_KINASE_RECEPTOR_SIGNALING_PATHWAY |
Semaphorin/Plexin/Neuropilin signaling
(SEMAPHORIN_PLEXIN_NEUROPILIN_SIGNALING) |
8 | GOBP_SEMAPHORIN_PLEXIN_SIGNALING_PATHWAYREACTOME_SEMAPHORIN_INTERACTIONS |
CHEMOKINE_GPCR_SIGNALING)Groups chemokine-receptor and related GPCR signalling axes that guide cell positioning and communication.
Verified membership: 1 category, 12 distinct core gene sets and 12 category assignments.
| Category | Core members | Representative member gene sets |
|---|---|---|
CXCR4/CXCL12 signaling (CXCR4_CXCL12_SIGNALING) |
12 | GOBP_CXCL12_ACTIVATED_CXCR4_SIGNALING_PATHWAYPID_CXCR4_PATHWAY |
The catalogue describes the dictionary. Study-specific NES, adjusted P values and leading edges are available in the report’s category evidence. In a single-analysis report, choose the analysis and collection, then select Category evidence in Section and the exact category in Category. See the report guide for the complete navigation and download distinctions. For custom resources and schema requirements, see Custom dictionaries and supercategories.