Sources
Here we list all the dataset sources used in the Bioteque resource. The scripts used to preprocess each dataset can be found here.
| Abbreviation | Association | Dataset | Source | In >=L2 | Preprocess |
|---|---|---|---|---|---|
| CHE-has-CPD | Compound has Chemical Entity | chebi | ChEBI | yes | link |
| CLL-ass-PWY | Cell associates Pathway | cosmic_mutsig | COSMIC | yes | link |
| CLL-bfn-(PGN)-pdw-GEN | Gene pertubed down by Perturbagen bad fitness Cell | achilles_HMZ | Harmonizome (Achilles) | link | |
| CLL-bfn-(PGN)-pdw-GEN | Gene pertubed down by Perturbagen bad fitness Cell | depmap_agreement_ccr | Depmap | yes | link |
| CLL-bfn-(PGN)-pdw-GEN | Gene pertubed down by Perturbagen bad fitness Cell | depmap_agreement_ceres | Depmap | yes | link |
| CLL-cnd-GEN | Cell copy number down Gene | cclecnv_HMZ | Harmonizome (CCLE) | link | |
| CLL-cnd-GEN | Cell copy number down Gene | gdsc1000_cfe | GDSC1000 | link | |
| CLL-cnu-GEN | Cell copy number up Gene | cclecnv_HMZ | Harmonizome (CCLE) | link | |
| CLL-cnu-GEN | Cell copy number up Gene | gdsc1000_cfe | GDSC1000 | link | |
| CLL-dwr-GEN | Cell downregulates Gene | ccle_rna | CCLE | yes | link |
| CLL-dwr-GEN | Cell downregulates Gene | gdsc1000_mrna | GDSC1000 | yes | link |
| CLL-gfn-(PGN)-pdw-GEN | Gene pertubed down by Perturbagen good fitness Cell | achilles_HMZ | Harmonizome (Achilles) | yes | link |
| CLL-has-DIS | Cell has Disease | cl_disease_clueio | CLUE | yes | link |
| CLL-has-TIS | Cell has Tissue | cl_tissue_clueio | CLUE | yes | link |
| CLL-hsp-CLL | Cell has parent Cell | cellosaurus | Cellosaurus | yes | link |
| CLL-mth-GEN | Cell methylates Gene | gdsc1000_cfe | GDSC1000 | link | |
| CLL-mut-GEN | Cell mutation Gene | ccle_mut | CCLE | link | |
| CLL-mut-GEN | Cell mutation Gene | cosmic_census | COSMIC | yes | link |
| CLL-mut-GEN | Cell mutation Gene | gdsc1000_cfe | GDSC1000 | yes | link |
| CLL-pab-GEN | Cell up protein Gene | ccle_proteome | CCLE | yes | link |
| CLL-pdf-GEN | Cell down protein Gene | ccle_proteome | CCLE | yes | link |
| CLL-sns-CPD | Cell sensitive Compound | ctrpv2_sens | PharmacoDB (CTRPv2) | yes | link |
| CLL-sns-CPD | Cell sensitive Compound | drugcell | Kuenzi et. al. (2020) (CTRPv2) | link | |
| CLL-sns-CPD | Cell sensitive Compound | gdsc1000_sens | PharmacoDB (GDSC1000) | yes | link |
| CLL-sns-CPD | Cell sensitive Compound | nci60_sens | CellMiner (NCI-60) | yes | link |
| CLL-sns-CPD | Cell sensitive Compound | prism | PRISM | yes | link |
| CLL-upr-GEN | Cell upregulates Gene | ccle_rna | CCLE | yes | link |
| CLL-upr-GEN | Cell upregulates Gene | gdsc1000_mrna | GDSC1000 | yes | link |
| CMP-has-GEN | Cell Compartment has Gene | jensencompartmentcurated | COMPARTMENTS | yes | link |
| CPD-cau-DIS | Compound causes Disease | ctdchemdis | CTD | link | |
| CPD-cau-DIS | Compound causes Disease | offsides | OffSIDES | yes | link |
| CPD-cau-DIS | Compound causes Disease | sider | SIDER | yes | link |
| CPD-ddi-CPD | Compound interacts Compound | drugbank_CC | Chemical Checker (Drugbank) | yes | link |
| CPD-dwr-GEN | Compound downregulates Gene | lincs_hetionet | Hetionet (LINCS) | yes | link |
| CPD-dws-GEN | Gene downregulatation sensitize Compound | pharmacodb_associations | PharmacoDB | yes | link |
| CPD-has-PHC | Compound has Pharmacologic Class | atc_drugs | Drugbank + Drugcentral + KEGG | yes | link |
| CPD-int-GEN | Compound interacts Gene | curated_targets | Drugbank + Repohub + PharmacoDB | yes | link |
| CPD-int-GEN | Compound interacts Gene | drugbank, drugbank_pd, drugbank_pk | Drugbank | link | |
| CPD-int-GEN | Compound interacts Gene | drugcentral | Drugcentral | link | |
| CPD-int-GEN | Compound interacts Gene | pharmacogenomic_targets | PharmacoDB | link | |
| CPD-int-GEN | Compound interacts Gene | repohub | Drug Repurposing Hub | link | |
| CPD-sim-CPD | Compound similar Compound | cc_sim | Chemical Checker | yes | link |
| CPD-sim-CPD | Compound similar Compound | fp2d_CC | Chemical Checker | yes | link |
| CPD-trt-DIS | Compound treats Disease | ctdchemdis | CTD | link | |
| CPD-trt-DIS | Compound treats Disease | repodb | repoDB | yes | link |
| CPD-upr-GEN | Compound upregulates Gene | lincs_hetionet | Hetionet (LINCS) | yes | link |
| CPD-ups-GEN | Gene upregulatation sensitize Compound | pharmacodb_associations | PharmacoDB | yes | link |
| DIS-ass-GEN | Gene associates Disease | ctddisease | CTD | link | |
| DIS-ass-GEN | Gene associates Disease | disgenet_befree | DisGeNET | link | |
| DIS-ass-GEN | Gene associates Disease | disgenet_curated | DisGeNET | yes | link |
| DIS-ass-GEN | Gene associates Disease | disgenet_inferred | DisGeNET | yes | link |
| DIS-ass-GEN | Gene associates Disease | opentargets | Open Targets | yes | link |
| DIS-cau-DIS | Disease causes Disease | disease_cau_symptom_hetionet | Hetionet | yes | link |
| DIS-dwr-GEN | Disease downregulates Gene | creeds_disease_curated | CREEDS | yes | link |
| DIS-has-TIS | Tissue has Disease | disease_loc_tissue_hetionet | Hetionet | yes | link |
| DIS-upr-GEN | Disease upregulates Gene | creeds_disease_curated | CREEDS | yes | link |
| DOM-has-GEN | Gene has Domain | interpro | Interpro | yes | link |
| GEN-ass-PWY | Gene associates Pathway | reactome | Reactome | yes | link |
| GEN-ass-TIS | Gene associates Tissue | jensentissuecurated | TISSUES | yes | link |
| GEN-cdp-GEN | Gene codepends Gene | depmap_agreement_ccr | Depmap | yes | link |
| GEN-cdp-GEN | Gene codepends Gene | depmap_agreement_ceres | Depmap | yes | link |
| GEN-cex-GEN | Gene coexpresses Gene | coexpressdb | CoexpressDB | yes | link |
| GEN-dph-GEN | Gene dephosphorylates Gene | omnipath | Omnipath | yes | link |
| GEN-dwr-GEN | Gene downregulates Gene | dorothea_AB | DoRothEA | yes | link |
| GEN-dwr-GEN | Gene downregulates Gene | dorothea_CD | DoRothEA | link | |
| GEN-dwr-PWY | Pathway downregulates Gene | progeny | PROGENy | yes | link |
| GEN-dwr-TIS | Tissue downregulates Gene | gtextissue_HMZ | Harmonizome (GTEx) | link | |
| GEN-dwr-TIS | Tissue downregulates Gene | hpa_rna_cons | HPA | yes | link |
| GEN-has-MFN | Gene has Molecular Function | gomf_goa_curated | GOA (GO) | yes | link |
| GEN-ngi-GEN | Gene negative GI Gene | eytan_2018 | Joo Sang Lee, et. al. (2018) | link | |
| GEN-ngi-GEN | Gene negative GI Gene | rauscher_2018 | Rauscher et. al. (2018) | yes | link |
| GEN-pab-TIS | Tissue protein abundance Gene | hpa_proteome | HPA | yes | link |
| GEN-pdf-TIS | Tissue protein deficiency Gene | hpa_proteome | HPA | yes | link |
| GEN-pdw-(PGN)-dwr/upr-GEN | Gene pertubed down by Perturbagen regulates Gene | lincs_sh_hetionet | Hetionet (LINCS) | yes | link |
| GEN-pgi-GEN | Gene positive GI Gene | rauscher_2018 | Rauscher et. al. (2018) | yes | link |
| GEN-pho-GEN | Gene phosphorylates Gene | kea_HMZ | Harmonizome (Lachmann et. al. (2009)) | link | |
| GEN-pho-GEN | Gene phosphorylates Gene | omnipath | Omnipath | yes | link |
| GEN-ppi-GEN | Gene ppi Gene | corum | CORUM | link | |
| GEN-ppi-GEN | Gene ppi Gene | hi_union | HuRI | link | |
| GEN-ppi-GEN | Gene ppi Gene | intact | IntAct | yes | link |
| GEN-ppi-GEN | Gene ppi Gene | omnipath | Omnipath | link | |
| GEN-ppi-GEN | Gene ppi Gene | string | STRING | yes | link |
| GEN-pup-(PGN)-dwr/upr-GEN | Gene pertubed up by Perturbagen regulates Gene | lincs_oe_hetionet | Hetionet (LINCS) | yes | link |
| GEN-reg-GEN | Gene regulates Gene | dorothea_AB | DoRothEA | yes | link |
| GEN-reg-GEN | Gene regulates Gene | dorothea_CD | DoRothEA | link | |
| GEN-upr-GEN | Gene upregulates Gene | dorothea_AB | DoRothEA | yes | link |
| GEN-upr-GEN | Gene upregulates Gene | dorothea_CD | DoRothEA | link | |
| GEN-upr-PWY | Pathway upregulates Gene | progeny | PROGENy | yes | link |
| GEN-upr-TIS | Tissue upregulates Gene | gtextissue_HMZ | Harmonizome (GTEx) | link | |
| GEN-upr-TIS | Tissue upregulates Gene | hpa_rna_cons | HPA | yes | link |
| TIS-hsp-TIS | Tissue has parent Tissue | bto | BTO | yes | link |
