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gsetdb.rat

GeneSetDB Rat 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.rat.rda
Fingerprint
9c0acac8
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
A list with no shape constraintsRows of cells of visibly different widths, one below the next, with nothing lining them up and nothing in them, and under them a small block with a header band: an element of a list can be another structure. There is no common length, so there is no row count.list

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 – 14,703
Total length
14,738
Nested rows
14,703
Nested columns
6
Elements
Element
Type
Distinct
Missing
Summary
species
character
1
0
3 characters
category
list
28
0
character
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
original
list
13,238
0
character
Element class
character
Element length
10 – 442
Total length
616,207
What is inside it
Element
Type
Distinct
Missing
Summary
T3DB_Cobalt(III)_fluoride
character
29
0
5 – 6 characters
STITCH_guanethidine(CID100003518)
character
18
0
5 – 6 characters
HPO_Abnormality_of_the_sense_of_smell_
character
13
0
5 – 6 characters
HPO_Sparse_hair_
character
30
0
5 – 6 characters
CTD_ABT-737
character
16
0
5 – 6 characters
MPO_abnormal_occipital_bone_morphology
character
18
0
5 – 6 characters
MPO_increased_pro-B_cell_number
character
30
0
5 – 6 characters
STITCH_dihydrosphingosine-1-phosphate(CID100000520)
character
14
0
5 – 6 characters
MPO_absent_tail
character
11
0
5 – 6 characters
STITCH_chlorophyll(CID005459387)
character
20
0
5 – 6 characters
GO_BP_telomere_maintenance_via_semi-conservative_replication_(GO:0032201)
character
20
0
5 – 6 characters
GO_BP_sex_differentiation_(GO:0007548)
character
24
0
5 – 6 characters
GO_BP_mammary_gland_alveolus_development_(GO:0060749)
character
15
0
5 – 6 characters
Reactome_MyD88_dependent_cascade_initiated_on_endosome
character
70
0
5 – 6 characters
MPO_increased_lung_compliance
character
11
0
5 – 6 characters
T3DB_Cadmium_bromide
character
18
0
5 – 6 characters
Reactome_CaM_pathway
character
22
0
5 – 6 characters
MPO_akinesia
character
17
0
5 – 6 characters
T3DB_Barium_cyanide
character
46
0
5 – 6 characters
MPO_reduced_fertility
character
142
0
5 – 6 characters
STITCH_p-nitrophenyl_phosphate(CID100000378)
character
11
0
5 – 6 characters
MATADOR_spironolactone
character
73
0
5 – 6 characters
WikiPathways_Wnt_Signaling_Pathway(WP428)
character
55
0
5 – 6 characters
STITCH_dextromethorphan(CID100003008)
character
22
0
5 – 6 characters
MPO_abnormal_intercostal_muscle_morphology
character
11
0
5 – 6 characters
STITCH_terbinafine(CID001549007)
character
14
0
5 – 6 characters
INOH_Galactose_metabolism
character
13
0
5 – 6 characters
MPO_abnormal_lymphocyte_morphology
character
35
0
5 – 6 characters
STITCH_methoxyresorufin(CID100119220)
character
10
0
5 – 6 characters
MPO_abnormal_nasal_capsule_morphology
character
22
0
5 – 6 characters
MPO_small_hippocampus
character
27
0
5 – 6 characters
SIDER_Diabetic_vascular_disorder
character
56
0
5 – 6 characters
MPO_abnormal_rod_electrophysiology
character
64
0
5 – 6 characters
GO_CC_clathrin_adaptor_complex_(GO:0030131)
character
16
0
5 – 6 characters
T3DB_Sodium_cobaltinitrite
character
32
0
5 – 6 characters
MATADOR_gabapentin
character
59
0
5 – 6 characters
CTD_romidepsin
character
33
0
5 – 6 characters
MATADOR_imipramine
character
17
0
5 – 6 characters
MPO_increased_brown_adipose_tissue_amount
character
30
0
5 – 6 characters
STITCH_ubiquinol(CID005280344)
character
23
0
5 – 6 characters
MPO_small_second_branchial_arch
character
16
0
5 – 6 characters
STITCH_chemotactic_peptide(CID100004364)
character
131
0
5 – 6 characters
MPO_abnormal_osteoclast_differentiation
character
68
0
5 – 6 characters
Reactome_Autodegradation_of_the_E3_ubiquitin_ligase_COP1
character
45
0
5 – 6 characters
STITCH_flavin_mononucleotide(CID000643976)
character
61
0
5 – 6 characters
STITCH_arsenic_trioxide(CID100014888)
character
66
0
5 – 6 characters
GO_CC_nuclear_chromatin_(GO:0000790)
character
65
0
5 – 6 characters
STITCH_pentoxyresorufin(CID000107683)
character
15
0
5 – 6 characters
MPO_abnormal_pulmonary_alveolus_morphology
character
111
0
5 – 6 characters
STITCH_glucose-6-phosphate(CID100000208)
character
67
0
5 – 6 characters
anno
list
6
0
nested·14,703 rows nested
Element length
14,703 – 14,703
Total length
88,218
Nested rows
14,703
What is inside it
Element
Type
Distinct
Missing
Summary
ID
factor
14,703
0
gsdb11gsdb101gsdb1001gsdb10001gsdb100001gsdb100011+14,697 more
Levels
14,703
Used
14,703
Rows per level, the 50 commonest of 14,703
gsdb11gsdb101gsdb1001gsdb10001gsdb100001gsdb100011gsdb100021gsdb100031gsdb100041gsdb100051gsdb100061gsdb100071gsdb100081gsdb100091gsdb10011gsdb100101gsdb100111gsdb100121gsdb100131gsdb100141gsdb100151gsdb100161gsdb100171gsdb100181gsdb100191gsdb10021gsdb100201gsdb100211gsdb100221gsdb100231gsdb100241gsdb100251gsdb100261gsdb100271gsdb100281gsdb100291gsdb10031gsdb100301gsdb100311gsdb100321gsdb100331gsdb100341gsdb100351gsdb100361gsdb100371gsdb100381gsdb100391gsdb10041gsdb100401gsdb100411
GeneSet
factor
14,703
0
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+14,697 more
Levels
14,703
Used
14,703
Rows per level, the 50 commonest of 14,703
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_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_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_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_Tumors1Biocarta_EGF_Signaling_Pathway1Biocarta_Eicosanoid_Metabolism1Biocarta_EPO_Signaling_Pathway1
NumGenes
integer
374
0
10 – 442mean 41.91
Min.
10
1st Qu.
14
Median
22
Mean
41.9103
3rd Qu.
43
Max.
442
Std. dev
55.2648
Skewness
3.617
Kurtosis
15.6
Outliers
1,5750 low · 1575 high
Category
factor
5
0
GeneSetDB Drug/Chemical5,952GeneSetDB Disease/Phenotype4,986GeneSetDB Gene Ontology2,129GeneSetDB Pathway1,436GeneSetDB Gene Regulation200
SourceDB
factor
28
0
STITCH3,879MPO2,894HPO1,479GO_BP1,371CTD915Reactome723+22 more
Levels
28
Used
28
Rows per level
STITCH3,879MPO2,894HPO1,479GO_BP1,371CTD915Reactome723T3DB718GO_MF463SIDER459GO_CC295MATADOR239PID193Biocarta174WikiPathways146DrugBank128TFactS101INOH73SMPDB73KEGG(Disease)63miRTarBase53EHMN51HumanCyc51MethyCancer49MicroCosm Targets45NetPath25CancerGenes23MethCancerDB19Rel/NF-kappaB target genes1
SourceURL
factor
26
0
http://stitch.embl.de/3,879http://www.informatics.jax.org/searches/MP_form.shtml2,894http://www.geneontology.org/2,129http://www.human-phenotype-ontology.org/1,479http://ctd.mdibl.org/915http://www.reactome.org/723+20 more
Levels
26
Used
26
Rows per level
http://stitch.embl.de/3,879http://www.informatics.jax.org/searches/MP_form.shtml2,894http://www.geneontology.org/2,129http://www.human-phenotype-ontology.org/1,479http://ctd.mdibl.org/915http://www.reactome.org/723http://www.t3db.org/718http://sideeffects.embl.de/459http://matador.embl.de/239http://pid.nci.nih.gov/193http://www.biocarta.com/174http://www.wikipathways.org/146http://www.drugbank.ca/128http://www.tfacts.org/101http://www.inoh.org/73http://www.smpdb.ca/73http://www.genome.jp/kegg/disease/63http://mirtarbase.mbc.nctu.edu.tw/53http://humancyc.org/51http://www.ehmn.bioinformatics.ed.ac.uk/51http://methycancer.psych.ac.cn/49http://www.ebi.ac.uk/enright-srv/microcosm/45http://www.netpath.org/25http://cbio.mskcc.org/CancerGenes/23http://www.methcancerdb.net/19http://bioinfo.lifl.fr/NF-KB/1
Every nested table has these 6 columns
  • ID
  • GeneSet
  • NumGenes
  • Category
  • SourceDB
  • SourceURL
Version history
VersionReleasedSizeChangeStored asConfidence
3.232026-04-284 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.222025-10-294 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.212025-04-154 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.202024-10-294 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.192024-04-304 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.182023-10-244 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.172023-04-254 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.162022-11-014 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.152022-04-264 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.142021-10-264 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.132021-05-194 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.122020-10-274 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.112020-04-274 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.102019-10-294 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.92019-05-024 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.82018-10-304 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.72018-04-304 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.62017-10-304 elementsUnchangedrda · xz
version 2 · 1.2 MB
exact
3.52017-08-164 elements–rda · xz
version 2 · 1.2 MB
exact

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