gsetdb.human
GeneSetDB Human Collections
Bundled with EGSEAdata · exported, loads via data()
Class
list
Elements
4
Missing
0
Format
rda · xz
version 2 · 1.2 MB
File
data/gsetdb.human.rda
Fingerprint
54e5a3d4
Format documented
Yes
Source
Araki Hiromitsu,Knapp Christoph,Tsai Peter and Print Cristin(2012), GeneSetDB: A comprehensive meta-database, statistical and visualisation framework for gene set analysis, FEBS Open Bio, 2, doi: 10.1016/j.fob.2012.04.003 Downloaded from http://www.genesetdb.auckland.ac.nz/
About this object
R's general-purpose container. Elements can be any type and any size. R object catalogue
Structure
Distinct
4
Nesting depth
2
Element length
1 – 16,638
Total length
16,673
Nested rows
16,638
Nested columns
6
Elements
Element
Type
Distinct
Missing
Summary
species
character
1
0
5 characters
categorylist280character
Element class
character
Element length
3 – 3
Total length
84
What is inside it
Element
Type
Distinct
Missing
Summary
Biocarta
character
3
0
8 – 24 characters
EHMN
character
3
0
17 – 40 characters
HumanCyc
character
3
0
17 – 42 characters
INOH
character
3
0
17 – 44 characters
NetPath
character
3
0
7 – 23 characters
PID
character
3
0
17 – 28 characters
Reactome
character
3
0
8 – 24 characters
WikiPathways
character
3
0
12 – 28 characters
CancerGenes
character
3
0
12 – 34 characters
KEGG(Disease)
character
3
0
12 – 34 characters
HPO
character
3
0
24 – 40 characters
MethCancerDB
character
3
0
27 – 34 characters
MethyCancer
character
3
0
11 – 31 characters
MPO
character
3
0
27 – 53 characters
SIDER
character
3
0
20 – 27 characters
CTD
character
3
0
21 – 35 characters
DrugBank
character
3
0
8 – 23 characters
MATADOR
character
3
0
23 – 52 characters
SMPDB
character
3
0
20 – 32 characters
STITCH
character
3
0
22 – 41 characters
T3DB
character
3
0
20 – 31 characters
MicroCosm Targets
character
3
0
17 – 43 characters
miRTarBase
character
3
0
10 – 34 characters
TFactS
character
3
0
6 – 25 characters
Rel/NF-kappaB target genes
character
3
0
25 – 29 characters
GO_BP
character
3
0
23 – 28 characters
GO_MF
character
3
0
22 – 28 characters
GO_CC
character
3
0
22 – 28 characters
originallist14,8700character
Element class
character
Element length
10 – 499
Total length
720,956
What is inside it
Element
Type
Distinct
Missing
Summary
T3DB_Cobalt(III)_fluoride
character
31
0
3 – 6 characters
STITCH_guanethidine(CID100003518)
character
21
0
3 – 4 characters
HPO_Abnormality_of_the_sense_of_smell_
character
14
0
3 – 6 characters
HPO_Sparse_hair_
character
38
0
3 – 9 characters
CTD_ABT-737
character
17
0
3 – 5 characters
HPO_Prominent_occiput_
character
10
0
4 – 9 characters
MPO_abnormal_occipital_bone_morphology
character
25
0
3 – 5 characters
MPO_increased_pro-B_cell_number
character
34
0
3 – 6 characters
STITCH_dihydrosphingosine-1-phosphate(CID100000520)
character
14
0
4 – 6 characters
MPO_absent_tail
character
14
0
4 – 6 characters
STITCH_chlorophyll(CID005459387)
character
22
0
3 – 6 characters
GO_BP_telomere_maintenance_via_semi-conservative_replication_(GO:0032201)
character
22
0
4 – 5 characters
GO_BP_sex_differentiation_(GO:0007548)
character
26
0
3 – 5 characters
GO_BP_mammary_gland_alveolus_development_(GO:0060749)
character
15
0
3 – 4 characters
Reactome_MyD88_dependent_cascade_initiated_on_endosome
character
81
0
3 – 6 characters
MPO_increased_lung_compliance
character
13
0
3 – 6 characters
T3DB_Cadmium_bromide
character
19
0
4 – 6 characters
T3DB_Azocyclotin
character
11
0
3 – 4 characters
Reactome_CaM_pathway
character
26
0
3 – 6 characters
MPO_akinesia
character
18
0
4 – 6 characters
T3DB_Barium_cyanide
character
56
0
3 – 9 characters
MPO_reduced_fertility
character
162
0
2 – 6 characters
STITCH_p-nitrophenyl_phosphate(CID100000378)
character
15
0
2 – 5 characters
MATADOR_spironolactone
character
90
0
3 – 9 characters
WikiPathways_Wnt_Signaling_Pathway(WP428)
character
60
0
3 – 5 characters
STITCH_L-CCG-I(CID100001271)
character
10
0
4 characters
STITCH_dextromethorphan(CID100003008)
character
25
0
4 – 6 characters
MPO_abnormal_intercostal_muscle_morphology
character
13
0
4 characters
STITCH_terbinafine(CID001549007)
character
16
0
4 – 6 characters
INOH_Galactose_metabolism
character
14
0
4 characters
MPO_abnormal_lymphocyte_morphology
character
40
0
3 – 5 characters
STITCH_methoxyresorufin(CID100119220)
character
13
0
3 – 5 characters
MPO_abnormal_nasal_capsule_morphology
character
23
0
3 – 6 characters
MPO_small_hippocampus
character
29
0
3 – 6 characters
SIDER_Diabetic_vascular_disorder
character
63
0
3 – 6 characters
MPO_abnormal_rod_electrophysiology
character
71
0
2 – 6 characters
GO_CC_clathrin_adaptor_complex_(GO:0030131)
character
20
0
3 – 6 characters
STITCH_N-oxalylglycine(CID003080614)
character
11
0
4 – 5 characters
T3DB_Sodium_cobaltinitrite
character
41
0
3 – 6 characters
MATADOR_gabapentin
character
65
0
2 – 6 characters
STITCH_ammonium_acetate(CID000012432)
character
10
0
4 – 9 characters
CTD_romidepsin
character
36
0
3 – 5 characters
MATADOR_imipramine
character
22
0
3 – 6 characters
MPO_increased_brown_adipose_tissue_amount
character
34
0
3 – 5 characters
STITCH_ubiquinol(CID005280344)
character
26
0
3 – 5 characters
MPO_small_second_branchial_arch
character
17
0
4 – 6 characters
STITCH_chemotactic_peptide(CID100004364)
character
144
0
3 – 6 characters
MPO_abnormal_osteoclast_differentiation
character
73
0
3 – 6 characters
miRTarBase_hsa-miR-199a-5p
character
10
0
3 – 5 characters
Reactome_Autodegradation_of_the_E3_ubiquitin_ligase_COP1
character
51
0
3 – 6 characters
annolist60nested·16,638 rows nested
Element length
16,638 – 16,638
Total length
99,828
Nested rows
16,638
What is inside it
Element
Type
Distinct
Missing
Summary
IDfactor16,6380gsdb11gsdb101gsdb1001gsdb10001gsdb100001gsdb100011+16,632 more
gsdb11gsdb101gsdb1001gsdb10001gsdb100001gsdb100011+16,632 more
Levels
16,638
Used
16,638
Rows per level, the 50 commonest of 16,638
gsdb11gsdb101gsdb1001gsdb10001gsdb100001gsdb100011gsdb100021gsdb100031gsdb100041gsdb100051gsdb100061gsdb100071gsdb100081gsdb100091gsdb10011gsdb100101gsdb100111gsdb100121gsdb100131gsdb100141gsdb100151gsdb100161gsdb100171gsdb100181gsdb100191gsdb10021gsdb100201gsdb100211gsdb100221gsdb100231gsdb100241gsdb100251gsdb100261gsdb100271gsdb100281gsdb100291gsdb10031gsdb100301gsdb100311gsdb100321gsdb100331gsdb100341gsdb100351gsdb100361gsdb100371gsdb100381gsdb100391gsdb10041gsdb100401gsdb100411
GeneSetfactor16,6380Biocarta_?-arrestins_in_GPCR_Desensitization1Biocarta_Acetylation_and_Deacetylation_of_RelA_in_The_Nucleus1Biocarta_Actions_of_Nitric_Oxide_in_the_Heart1Biocarta_Activation_of_Csk_by_cAMP-dependent_Protein_Kinase_Inhibits_Signaling_through_the_T_Cell_Receptor1Biocarta_Acute_Myocardial_Infarction1Biocarta_Adhesion_and_Diapedesis_of_Granulocytes1+16,632 more
Biocarta_?-arrestins_in_GPCR_Desensitization1Biocarta_Acetylation_and_Deacetylation_of_RelA_in_The_Nucleus1Biocarta_Actions_of_Nitric_Oxide_in_the_Heart1Biocarta_Activation_of_Csk_by_cAMP-dependent_Protein_Kinase_Inhibits_Signaling_through_the_T_Cell_Receptor1Biocarta_Acute_Myocardial_Infarction1Biocarta_Adhesion_and_Diapedesis_of_Granulocytes1+16,632 more
Levels
16,638
Used
16,638
Rows per level, the 50 commonest of 16,638
Biocarta_?-arrestins_in_GPCR_Desensitization1Biocarta_Acetylation_and_Deacetylation_of_RelA_in_The_Nucleus1Biocarta_Actions_of_Nitric_Oxide_in_the_Heart1Biocarta_Activation_of_Csk_by_cAMP-dependent_Protein_Kinase_Inhibits_Signaling_through_the_T_Cell_Receptor1Biocarta_Acute_Myocardial_Infarction1Biocarta_Adhesion_and_Diapedesis_of_Granulocytes1Biocarta_Adhesion_and_Diapedesis_of_Lymphocytes1Biocarta_ADP-Ribosylation_Factor1Biocarta_Agrin_in_Postsynaptic_Differentiation1Biocarta_AKAP95_role_in_mitosis_and_chromosome_dynamics1Biocarta_AKT_Signaling_Pathway1Biocarta_ALK_in_cardiac_myocytes1Biocarta_Angiotensin_II_mediated_activation_of_JNK_Pathway_via_Pyk2_dependent_signaling1Biocarta_Antigen_Dependent_B_Cell_Activation1Biocarta_Apoptotic_Signaling_in_Response_to_DNA_Damage1Biocarta_Aspirin_Blocks_Signaling_Pathway_Involved_in_Platelet_Activation1Biocarta_ATM_Signaling_Pathway1Biocarta_B_Cell_Survival_Pathway1Biocarta_B_Lymphocyte_Cell_Surface_Molecules1Biocarta_BCR_Signaling_Pathway1Biocarta_Bioactive_Peptide_Induced_Signaling_Pathway1Biocarta_Bone_Remodelling1Biocarta_BTG_family_proteins_and_cell_cycle_regulation1Biocarta_Cadmium_induces_DNA_synthesis_and_proliferation_in_macrophages1Biocarta_CARM1_and_Regulation_of_the_Estrogen_Receptor1Biocarta_Caspase_Cascade_in_Apoptosis1Biocarta_CBL_mediated_ligand-induced_downregulation_of_EGF_receptors1Biocarta_CCR3_signaling_in_Eosinophils1Biocarta_CD40L_Signaling_Pathway1Biocarta_Cell_Cycle:_G1/S_Check_Point_1Biocarta_Cell_Cycle:_G2/M_Checkpoint1Biocarta_Cell_to_Cell_Adhesion_Signaling1Biocarta_Cells_and_Molecules_involved_in_local_acute_inflammatory_response1Biocarta_Ceramide_Signaling_Pathway1Biocarta_Chaperones_modulate_interferon_Signaling_Pathway1Biocarta_Chromatin_Remodeling_by_hSWI/SNF_ATP-dependent_Complexes1Biocarta_Classical_Complement_Pathway1Biocarta_Complement_Pathway1Biocarta_Control_of_Gene_Expression_by_Vitamin_D_Receptor1Biocarta_Control_of_skeletal_myogenesis_by_HDAC_&_calcium/calmodulin-dependent_kinase_(CaMK)1Biocarta_Corticosteroids_and_cardioprotection1Biocarta_CTCF:_First_Multivalent_Nuclear_Factor1Biocarta_CTL_mediated_immune_response_against_target_cells_1Biocarta_CXCR4_Signaling_Pathway1Biocarta_Cyclins_and_Cell_Cycle_Regulation1Biocarta_Cytokine_Network1Biocarta_Cytokines_and_Inflammatory_Response1Biocarta_D4-GDI_Signaling_Pathway1Biocarta_Dendritic_cells_in_regulating_TH1_and_TH2_Development1Biocarta_Downregulated_of_MTA-3_in_ER-negative_Breast_Tumors1
NumGenesinteger417010 – 499mean 43.33
Min.
10
1st Qu.
14
Median
22
Mean
43.3319
3rd Qu.
44
Max.
499
Std. dev
60.9905
Skewness
3.899
Kurtosis
18.49
Outliers
1,7820 low · 1782 high
Category
factor
5
0
GeneSetDB Drug/Chemical7,032GeneSetDB Disease/Phenotype5,425GeneSetDB Gene Ontology2,431GeneSetDB Pathway1,535GeneSetDB Gene Regulation215
SourceDBfactor280STITCH4,616MPO3,134HPO1,639GO_BP1,567CTD1,047T3DB846+22 more
STITCH4,616MPO3,134HPO1,639GO_BP1,567CTD1,047T3DB846+22 more
Levels
28
Used
28
Rows per level
STITCH4,616MPO3,134HPO1,639GO_BP1,567CTD1,047T3DB846Reactome776GO_MF534SIDER473GO_CC330MATADOR266Biocarta197PID195DrugBank176WikiPathways152TFactS108KEGG(Disease)81SMPDB81INOH76miRTarBase62HumanCyc59EHMN55MethyCancer54MicroCosm Targets44NetPath25CancerGenes23MethCancerDB21Rel/NF-kappaB target genes1
SourceURLfactor260http://stitch.embl.de/4,616http://www.informatics.jax.org/searches/MP_form.shtml3,134http://www.geneontology.org/2,431http://www.human-phenotype-ontology.org/1,639http://ctd.mdibl.org/1,047http://www.t3db.org/846+20 more
http://stitch.embl.de/4,616http://www.informatics.jax.org/searches/MP_form.shtml3,134http://www.geneontology.org/2,431http://www.human-phenotype-ontology.org/1,639http://ctd.mdibl.org/1,047http://www.t3db.org/846+20 more
Levels
26
Used
26
Rows per level
http://stitch.embl.de/4,616http://www.informatics.jax.org/searches/MP_form.shtml3,134http://www.geneontology.org/2,431http://www.human-phenotype-ontology.org/1,639http://ctd.mdibl.org/1,047http://www.t3db.org/846http://www.reactome.org/776http://sideeffects.embl.de/473http://matador.embl.de/266http://www.biocarta.com/197http://pid.nci.nih.gov/195http://www.drugbank.ca/176http://www.wikipathways.org/152http://www.tfacts.org/108http://www.genome.jp/kegg/disease/81http://www.smpdb.ca/81http://www.inoh.org/76http://mirtarbase.mbc.nctu.edu.tw/62http://humancyc.org/59http://www.ehmn.bioinformatics.ed.ac.uk/55http://methycancer.psych.ac.cn/54http://www.ebi.ac.uk/enright-srv/microcosm/44http://www.netpath.org/25http://cbio.mskcc.org/CancerGenes/23http://www.methcancerdb.net/21http://bioinfo.lifl.fr/NF-KB/1
Every nested table has these 6 columns
- ID
- GeneSet
- NumGenes
- Category
- SourceDB
- SourceURL
Version history
| Version | Released | Size | Change | Stored as | Confidence |
|---|---|---|---|---|---|
| 3.23 | 2026-04-28 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.22 | 2025-10-29 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.21 | 2025-04-15 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.20 | 2024-10-29 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.19 | 2024-04-30 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.18 | 2023-10-24 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.17 | 2023-04-25 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.16 | 2022-11-01 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.15 | 2022-04-26 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.14 | 2021-10-26 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.13 | 2021-05-19 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.12 | 2020-10-27 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.11 | 2020-04-27 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.10 | 2019-10-29 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.9 | 2019-05-02 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.8 | 2018-10-30 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.7 | 2018-04-30 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.6 | 2017-10-30 | 4 elements | Unchanged | rda · xz version 2 · 1.2 MB | exact |
| 3.5 | 2017-08-16 | 4 elements | – | rda · xz version 2 · 1.2 MB | exact |