Initial commit

README.md

+# Using DISNET towards COVID-19 drug repositioning
+
+This repository is structured as follows:
+
+>```
+>disnet_covid_paper
+>├── counts
+>│	├── count_dbc_path4.tsv 
+>│	├── count_dpc_path2.tsv
+>│	├── count_drugs_path1.tsv
+>│	├── count_drugs_path2.tsv
+>│	├── count_drugs_path3.tsv
+>│	├── count_drugs_path4.tsv
+>│	└── count_drugs_path5.tsv
+>├── paths
+>│	├── covid_genes.tsv
+>│	├── covid_symptoms.tsv
+>│	├── diseases_bio_covid.tsv
+>│	├── diseases_pheno_covid.tsv
+>│	├── genes_dpc.tsv
+>│	├── targets_gc.tsv
+>│	└── targets_dpc.tsv
+>├── results
+>│	├── drugs_allpaths.tsv
+>│	├── drugs_path1.tsv
+>│	├── drugs_path2.tsv
+>│	├── drugs_path3.tsv
+>│	├── drugs_path4.tsv
+>│	└── drugs_path5.tsv
+>├── paths-pipeline.svg
+>└── README.md
+>```
+
+Two important concepts to clarify:
+
+- **dpc**: stands for those diseases phenotypically related to COVID-19, that is, that have common symptoms.
+
+- **dbc**: stands for those diseases biologically related to COVID-19, that is, that have related genes in common.
+
+
+## counts
+
+Files with different counts along the five paths of information.
+
+- **count_dbc_path4.tsv** 
+
+| disease_id|disease_name|count_genes|
+|:-:|:-:|:-:|
+|Identifiers of diseases that have biological resemblance with COVID-19 (dbc), i.e. that have genes in common|Names of the diseases|Number of shared genes between diseases (dbc) and COVID-19|
+
+- **count_dpc_path2.tsv** 
+
+|disease_name|count_symptoms|
+|:-:|:-:|
+|Names of diseases that have phenotypical resemblance with COVID-19 (dpc), i.e. that have symptoms in common|Number of shared symptoms between diseases (dpc) and COVID-19|
+
+- **count_drugs_path1.tsv** 
+
+|drug_id|drug_name|count_symptoms|
+|:-:|:-:|:-:|
+|Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of COVID related symptoms to which drugs are indicated for|
+
+- **count_drugs_path2.tsv** 
+
+|drug_id|drug_name|count_dpc|
+|:-:|:-:|:-:|
+|Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of diseases (dpc) that are associated to the drugs|
+
+- **count_drugs_path3.tsv**
+
+|drug_id|drug_name|count_targets|
+|:-:|:-:|:-:|
+|Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of targets associated to each drug that are related to diseases that have phenotypical resemblance with COVID-19 (dpc)|
+
+- **count_drugs_path4.tsv** 
+
+|drug_id|drug_name|count_dbc|
+|:-:|:-:|:-:|
+|Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of diseases (dbc) that are associated to the drugs|
+
+- **count_drugs_path5.tsv**
+
+|drug_id|drug_name|count_targets|
+|:-:|:-:|:-:|
+|Identifiers of drugs potentially repurposable for COVID-19|Names of the drugs|Number of targets related to COVID-19 genes that are associated to each drug|
+
+
+## paths
+
+Files with different data obtained in the paths of information.
+
+- **covid_genes.tsv** : genes that are related to COVID-19
+
+|gene_id|gene_symbol|gene_name|
+|:-:|:-:|:-:|
+|NCBI identifiers of genes|Symbols of the genes|Complete name of the genes|
+
+- **covid_symptoms.tsv** : symptoms that are related to COVID-19
+
+|symptom_cui|symptom_name|source|
+|:-:|:-:|:-:|
+|UMLS CUIs identifying COVID-19 symptoms|Names of the symptoms|Textual source from which the symptoms have been extracted|
+
+- **diseases_bio_covid.tsv** : (dbc) diseases that have a biological resemblance to COVID-19, that is, that have common related genes with COVID-19.
+
+|disease_cui|disease_name|
+|:-:|:-:|
+|UMLS CUIs identifying diseases (dbc)|Names of the diseases|
+
+- **diseases_pheno_covid.tsv**: (dpc) diseases that have a phenotypical resemblance to COVID-19, that is, that have common related symptoms with COVID-19.
+
+|disease_name|
+|:-:|
+|Names of the diseases (dpc)|
+
+- **genes_dpc.tsv**:  genes related to diseases dpc and that are associated to targets and drugs potentially repurposable for COVID-19.
+
+|gene_id|gene_symbol|gene_name|
+|:-:|:-:|:-:|
+|NCBI identifiers of genes|Symbols of the genes|Complete name of the genes|
+
+- **targets_gc.tsv**: targets related to COVID associated genes, and that are also related to drugs potentially repurposable for COVID-19. 
+
+|chembl_id|uniprot_id|
+|:-:|:-:|
+|Targets identified by CHEMBL identifiers|Targets identified by UniProt accession numbers|
+
+- **targets_dpc.tsv**: targets related to dpc associated genes, that are also related to drugs potentially repurposable for COVID-19.
+
+|chembl_id|uniprot_id|
+|:-:|:-:|
+|Targets identified by CHEMBL identifiers|Targets identified by UniProt accession numbers|
+
+
+
+
+## results
+
+Files with lists of drugs derived from the different paths of information.
+
+- **drugs_allpaths.tsv**: drugs in all paths with the list of related targets (represented with the gene symbol).
+
+|drug_id|drug_name|covid_symptoms_path1|dpc_path2|dpc_genes_path3|dbc_path4|covid_genes_path5|
+|:-:|:-:|:-:|:-:|:-:|:-:|:-:|
+|Drug CHEMBL identifier|Drug name|COVID-19 symptom(s) to which the drug is indicated for|Disease(s) (dpc) phenotypically similar to COVID-19 related to the drug [Number of shared symptoms between COVID-19 and the disease]|Targets (represented with NCBI gene symbols) related to diseases (dbc) that are associated to the drug [Number of diseases (dpc) phenotypically similar to COVID-19 that are related to the target]|Diseases (dbc) biologically similar to COVID-19 related to the drug [Number of shared genes between COVID-19 and the disease]|Target(s) (represented with NCBI gene symbols) related to COVID-19 associated to the drug|
+
+- **drugs_path1.tsv**: list of drugs derived from Path 1. 
+
+|drug_id|drug_name|
+|:-:|:-:|
+|Drug CHEMBL identifier|Drug name|
+
+- **drugs_path2.tsv**: list of drugs derived from Path 2.
+
+|drug_id|drug_name|
+|:-:|:-:|
+|Drug CHEMBL identifier|Drug name|
+
+- **drugs_path3.tsv**: list of drugs derived from Path 3. 
+
+|drug_id|drug_name|
+|:-:|:-:|
+|Drug CHEMBL identifier|Drug name|
+
+- **drugs_path4.tsv**: list of drugs derived from Path 4. 
+
+|drug_id|drug_name|
+|:-:|:-:|
+|Drug CHEMBL identifier|Drug name|
+
+- **drugs_path5.tsv**: list of drugs derived from Path 5. 
+
+|drug_id|drug_name|
+|:-:|:-:|
+|Drug CHEMBL identifier|Drug name|
+
+
+## paths-pipeline.svg
+Graphical representation of the different paths of information followed.
\ No newline at end of file

counts/count_drugs_path5.tsv

+CHEMBL12856	INAMRINONE	1
+CHEMBL2103749	BIVALIRUDIN	1
+CHEMBL413	SIROLIMUS	1
+CHEMBL1422	SITAGLIPTIN	1
+CHEMBL2105759	BARICITINIB	1
+CHEMBL425	OLSALAZINE	1
+CHEMBL1201011	QUINAPRIL HYDROCHLORIDE	1
+CHEMBL1435	CEFAZOLIN	1
+CHEMBL2108147	STREPTOKINASE	1
+CHEMBL431	SPIRAPRIL	1
+CHEMBL1201420	UROKINASE	1
+CHEMBL1513	IRBESARTAN	1
+CHEMBL2108667	YTTRIUM Y 90 IBRITUMOMAB TIUXETAN	1
+CHEMBL1201550	DENILEUKIN DIFTITOX	1
+CHEMBL1560	CAPTOPRIL	1
+CHEMBL2108791	TENECTEPLASE	1
+CHEMBL494	ILOPROST	1
+CHEMBL1201576	RITUXIMAB	1
+CHEMBL1592	QUINAPRIL	1
+CHEMBL227529	ALOGLIPTIN BENZOATE	1
+CHEMBL522038	XIMELAGATRAN	1
+CHEMBL1017	TELMISARTAN	1
+CHEMBL1201593	ALTEPLASE	1
+CHEMBL1668	RESCINNAMINE	1
+CHEMBL3039598	FOSINOPRIL	1
+CHEMBL577	ENALAPRILAT	1
+CHEMBL1089	PHENELZINE	1
+CHEMBL1201606	IBRITUMOMAB TIUXETAN	1
+CHEMBL1743029	IBALIZUMAB	1
+CHEMBL325041	BORTEZOMIB	1
+CHEMBL679	EPINEPHRINE	1
+CHEMBL1166	ARGATROBAN	1
+CHEMBL1201666	LEPIRUDIN	1
+CHEMBL1743068	SECUKINUMAB	1
+CHEMBL3545432	IXAZOMIB CITRATE	1
+CHEMBL813	EPROSARTAN	1
+CHEMBL1200534	MOEXIPRIL HYDROCHLORIDE	1
+CHEMBL1201831	CERTOLIZUMAB PEGOL	1
+CHEMBL1789941	RUXOLITINIB	1
+CHEMBL385517	SAXAGLIPTIN	1
+CHEMBL877	TRANEXAMIC ACID	1
+CHEMBL1201836	OFATUMUMAB	1
+CHEMBL1256391	PIRFENIDONE	1
+CHEMBL191	LOSARTAN	1
+CHEMBL3989977	EMAPALUMAB	1
+CHEMBL1200807	NORELGESTROMIN	1
+CHEMBL1334033	PERHEXILINE MALEATE	1
+CHEMBL2103795	AZILSARTAN KAMEDOXOMIL	1
+CHEMBL413965	FELBINAC	1
+CHEMBL1200983	GALLIUM NITRATE	1
+CHEMBL142703	VILDAGLIPTIN	1
+CHEMBL2107885	RETEPLASE	1
+CHEMBL4297723	CEMIPLIMAB	1
+CHEMBL1201174	SITAGLIPTIN PHOSPHATE	1
+CHEMBL1479	DANAZOL	1
+CHEMBL2108247	CLOVE OIL	1
+CHEMBL43452	POMALIDOMIDE	1
+CHEMBL1201438	ALDESLEUKIN	1
+CHEMBL1519	TRANDOLAPRIL	1
+CHEMBL2108730	SARILUMAB	1
+CHEMBL49080	CLENBUTEROL	1
+CHEMBL1201554	ANTITHROMBIN ALFA	1
+CHEMBL1581	PERINDOPRIL	1
+CHEMBL2109624	CAPLACIZUMAB	1
+CHEMBL1201580	ADALIMUMAB	1
+CHEMBL1615369	DABIGATRAN ETEXILATE MESYLATE	1
+CHEMBL237500	LINAGLIPTIN	1
+CHEMBL539697	DABIGATRAN ETEXILATE	1
+CHEMBL1201604	TOSITUMOMAB	1
+CHEMBL1694	BENAZEPRIL HYDROCHLORIDE	1
+CHEMBL3137343	PEMBROLIZUMAB	1
+CHEMBL578	ENALAPRIL	1
+CHEMBL1115	PYRIDOSTIGMINE	1
+CHEMBL1201619	APROTININ	1
+CHEMBL1743034	IXEKIZUMAB	1
+CHEMBL3544986	PERINDOPRIL ARGININE	1
+CHEMBL1168	RAMIPRIL	1
+CHEMBL1201743	SAXAGLIPTIN HYDROCHLORIDE	1
+CHEMBL1743070	SILTUXIMAB	1
+CHEMBL3707226	DEFIBROTIDE SODIUM	1
+CHEMBL838	BENAZEPRIL	1
+CHEMBL1200659	ENALAPRIL MALEATE	1
+CHEMBL1201833	GOLIMUMAB	1
+CHEMBL1795071	RUXOLITINIB PHOSPHATE	1
+CHEMBL3989406	ENALAPRILAT	1
+CHEMBL995	LOSARTAN POTASSIUM	1
+CHEMBL1200686	PIMECROLIMUS	1
+CHEMBL1265	ADAPALENE	1
+CHEMBL2028661	AZILSARTAN MEDOXOMIL	1
+CHEMBL408403	ANGIOTENSIN II	1
+CHEMBL1200831	SPIRAPRIL HYDROCHLORIDE	1
+CHEMBL14060	PHENOL	1
+CHEMBL419213	LISINOPRIL	1
+CHEMBL1200987	EPROSARTAN MESYLATE	1
+CHEMBL1434	MINOCYCLINE	1
+CHEMBL2108041	OCRELIZUMAB	1
+CHEMBL43	AMSACRINE	1
+CHEMBL1201182	TEMSIROLIMUS	1
+CHEMBL1487	ATORVASTATIN	1
+CHEMBL2108250	ANISTREPLASE	1
+CHEMBL451887	CARFILZOMIB	1
+CHEMBL1201439	BASILIXIMAB	1
+CHEMBL1535	HYDROXYCHLOROQUINE	1
+CHEMBL2108738	NIVOLUMAB	1
+CHEMBL1201572	ETANERCEPT	1
+CHEMBL221959	TOFACITINIB	1
+CHEMBL515606	CILAZAPRIL	1
+CHEMBL1014	CANDESARTAN CILEXETIL	1
+CHEMBL1201581	INFLIXIMAB	1
+CHEMBL1639	ALISKIREN	1
+CHEMBL3039596	FOSINOPRIL SODIUM	1
+CHEMBL55400	PROFLAVINE	1
+CHEMBL1069	VALSARTAN	1
+CHEMBL1201605	DACLIZUMAB	1
+CHEMBL1730	CEFOTAXIME	1
+CHEMBL590	MENADIONE	1
+CHEMBL1165	MOEXIPRIL	1
+CHEMBL1201662	DESIRUDIN	1
+CHEMBL1743048	OBINUTUZUMAB	1
+CHEMBL3545059	ALISKIREN FUMARATE	1
+CHEMBL802	MINOXIDIL	1
+CHEMBL1200343	PERINDOPRIL ERBUMINE	1
+CHEMBL175	DEXIBUPROFEN	1
+CHEMBL376359	ALOGLIPTIN	1
+CHEMBL863	CYSTEINE	1
+CHEMBL1200670	SARALASIN ACETATE	1
+CHEMBL1201834	CANAKINUMAB	1
+CHEMBL1237022	TOCILIZUMAB	1
+CHEMBL1908360	EVEROLIMUS	1
+CHEMBL3989932	ANGIOTENSIN II ACETATE	1
+CHEMBL1200692	OLMESARTAN MEDOXOMIL	1
+CHEMBL468	THALIDOMIDE	2
+CHEMBL1200679	ZINC CHLORIDE	2
+CHEMBL502	DONEPEZIL	2
+CHEMBL1046	AMINOCAPROIC ACID	2
+CHEMBL76	CHLOROQUINE	2
+CHEMBL1237	LISINOPRIL	2
+CHEMBL493287	GLUCOSAMINE	2
+CHEMBL1201830	RILONACEPT	2
+CHEMBL2103830	FOSTAMATINIB	3
+CHEMBL1590	PSEUDOEPHEDRINE	3
+CHEMBL3187723	BINIMETINIB	3
+CHEMBL1200928	ZINC ACETATE	4

paths/covid_genes.tsv

+gene_id	gene_symbol	gene_name
+28	ABO	"ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase"
+183	AGT	angiotensinogen
+185	AGTR1	"angiotensin II receptor type 1"
+213	ALB	albumin
+268	AMH	"anti-Mullerian hormone"
+682	BSG	"basigin (Ok blood group)"
+796	CALCA	"calcitonin related polypeptide alpha"
+920	CD4	"CD4 molecule"
+925	CD8A	"CD8a molecule"
+931	MS4A1	"membrane spanning 4-domains A1"
+1401	CRP	"C-reactive protein"
+1437	CSF2	"colony stimulating factor 2"
+1506	CTRL	"chymotrypsin like"
+1514	CTSL	"cathepsin L"
+1636	ACE	"angiotensin I converting enzyme"
+1803	DPP4	"dipeptidyl peptidase 4"
+2147	F2	"coagulation factor II, thrombin"
+2152	F3	"coagulation factor III, tissue factor"
+2475	MTOR	"mechanistic target of rapamycin kinase"
+2539	G6PD	"glucose-6-phosphate dehydrogenase"
+2805	GOT1	"glutamic-oxaloacetic transaminase 1"
+2875	GPT	"glutamic--pyruvic transaminase"
+3107	HLA-C	"major histocompatibility complex, class I, C"
+3439	IFNA1	"interferon alpha 1"
+3456	IFNB1	"interferon beta 1"
+3458	IFNG	"interferon gamma"
+3552	IL1A	"interleukin 1 alpha"
+3553	IL1B	"interleukin 1 beta"
+3558	IL2	"interleukin 2"
+3559	IL2RA	"interleukin 2 receptor subunit alpha"
+3569	IL6	"interleukin 6"
+3570	IL6R	"interleukin 6 receptor"
+3576	CXCL8	"C-X-C motif chemokine ligand 8"
+3586	IL10	"interleukin 10"
+3605	IL17A	"interleukin 17A"
+3627	CXCL10	"C-X-C motif chemokine ligand 10"
+3630	INS	insulin
+3716	JAK1	"Janus kinase 1"
+3827	KNG1	"kininogen 1"
+4045	LSAMP	"limbic system associated membrane protein"
+4153	MBL2	"mannose binding lectin 2"
+4790	NFKB1	"nuclear factor kappa B subunit 1"
+5045	FURIN	"furin, paired basic amino acid cleaving enzyme"
+5131	PDB1	"Paget disease of bone 1"
+5133	PDCD1	"programmed cell death 1"
+5327	PLAT	"plasminogen activator, tissue type"
+5340	PLG	plasminogen
+5707	PSMD1	"proteasome 26S subunit, non-ATPase 1"
+5972	REN	renin
+6252	RTN1	"reticulon 1"
+6301	SARS	"seryl-tRNA synthetase"
+6347	CCL2	"C-C motif chemokine ligand 2"
+7113	TMPRSS2	"transmembrane serine protease 2"
+7124	TNF	"tumor necrosis factor"
+7137	TNNI3	"troponin I3, cardiac type"
+7450	VWF	"von Willebrand factor"
+9372	ZFYVE9	"zinc finger FYVE-type containing 9"
+27074	LAMP3	"lysosomal associated membrane protein 3"
+51497	NELFCD	"negative elongation factor complex member C/D"
+51517	NCKIPSD	"NCK interacting protein with SH3 domain"
+54806	AHI1	"Abelson helper integration site 1"
+55835	CENPJ	"centromere protein J"
+57142	RTN4	"reticulon 4"
+59272	ACE2	"angiotensin I converting enzyme 2"
+92521	SPECC1	"sperm antigen with calponin homology and coiled-coil domains 1"
+114548	NLRP3	"NLR family pyrin domain containing 3"
+388007	SERPINA13P	"serpin family A member 13, pseudogene"
+43740568	S	"surface glycoprotein"
+43740570	E	"envelope protein"
+43740575	N	"nucleocapsid phosphoprotein"
+43740577	ORF8	"ORF8 protein"
+43740578	ORF1ab	"ORF1a polyprotein;ORF1ab polyprotein"
+101927746	EMSLR	"E2F1 mRNA stabilizing lncRNA"
+102723407	LOC102723407	"immunoglobulin heavy variable 4-38-2-like"
+102724971	LOC102724971	"putative V-set and immunoglobulin domain-containing-like protein IGHV4OR15-8"