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Harmonizome-KG: Visualizing Gene-Term Relations Across 120+ Datasets

Using Harmonizome-KG

1. Creating a subnetwork

1.1 One-term Search

One-Term Search

To begin a query with , the UI requires the input of a starting dataset or gene. In the dropdown boxes on the left, you can select the dataset or gene you would like to look up and choose whether you would like to search by ID or label. Then you will need to enter the ID or label underneath.

For example, if we want to search up a gene and we know the label, we can select "gene" in the first dropdown box and select "label". Then we can enter the label "STAT3" and the following subnetwork will be generated automatically showing a few related entities to the gene!

1.2 Refining the search by relation

Refine by Dropdown

With the Term & Gene search, you can refine your results in various ways. In the picture above, we want to see the phenotypes from GWASdb Catalog that the search term is related to. To do this, we can use the "Select Relation" dropdown to select the relation "has_phenotype_(GWASdb Phenotype)". The generated graph shows phenotypes from GWASdb in relation to the searched gene (STAT3) in yellow.

1.3 Refining the search by resource icon

Refine by Icon

You can also limit the subnetwork's results by specifying which resources' entities you would like to see in the subnetwork! You can do this by clicking on one of the resource icons at the top of the page. In the picture above, we clicked the "TCGA" icon to generate the subnetwork with relations between genes and tissue samples from TCGA. If you would specifically like to see the tissue samples in which the gene is under-expressed in, you can "X" out the "over-expressed in" relation next to the relation dropdown box.

1.4 Changing the subnetwork display

Toolbar

With Term & Gene Search, there are various ways to change the way the subnetwork is displayed and saved! You can use the slider bar above the network view to increase or decrease the maximum amount of relations you wish to display for each relation type. For example, sliding the bar to "5" will display at most 5 edges of each relation. On the right, the full-screen icon will display the subnetwork in full-screen. The first two mini icons next to the full-screen icon represent viewing the subnetwork as 1. a graph or 2. a table. The next two icons represent two ways to save the subnetwork: 1. as tsv files separated by nodes and edges or 2. as a png. The last group of icons refer to ways to change the network view: 1. enabling tooltips which each node's metadata as you hover over them; 2. switching the graph layout to be i. force-directed, ii. hierarchichal, and iii. geometric; 3. showing edge labels; and 4. showing a legend to see the different node types each color represents.

1.5 Two-term Search

Two-Term Search

Generate a more complex subnetwork with Gene and Term Search's Two-Term Search! First enter a starting entity similar to the one-term search and then toggle "end node". This will produce another node field for you to enter the ending entity. In the picture above, we wanted to look up two genes at once (STAT3 and APOE) to see some of the biological entities they are both related to. The generated subnetwork shows a few of these common entities, colored differently by the dataset they come from. You can increase the size of the graph to see more of these entities!

Processed Datasets Included in Harmonizome-KG

Dataset Source Type Target Type Resource Link Genes Terms Edges
Achilles gene cell line https://depmap.org/portal/achilles/ 4831 216 104046
HuBMAP Azimuth Cell Type gene cell type https://hubmapconsortium.org/ 3560 1426 13794
Biocarta gene pathway https://www.liebertpub.com/doi/pdf/10.1089/152791601750294344 1397 254 4509
BioGPS Human gene cell type or tissue http://biogps.org/#goto=welcome 16379 84 205445
BioGPS Mouse gene cell type or tissue http://biogps.org/#goto=welcome 15437 74 170878
BioGPS NCI-60 gene cell line http://biogps.org/#goto=welcome 12628 93 204284
ABA Adult Human gene tissue https://portal.brain-map.org/ 17979 414 1115464
ABA Adult Mouse gene tissue https://portal.brain-map.org/ 14248 2219 3178416
ABA Developmental Human Microarray gene tissue sample https://portal.brain-map.org/ 17238 492 1270962
ABA Developmental Human RNA Seq gene tissue sample https://portal.brain-map.org/ 15072 524 1183125
ABA Prenatal Human gene tissue https://portal.brain-map.org/ 18949 516 1464892
CCLE CNV gene cell line https://portals.broadinstitute.org/ccle 23264 1036 1148953
CCLE Gene Expression gene cell line https://portals.broadinstitute.org/ccle 18025 1035 751223
CCLE Mutations gene cell line https://portals.broadinstitute.org/ccle 1667 904 105921
CCLE Proteomics gene cell line https://portals.broadinstitute.org/ccle 8959 375 122680
CellMarker gene cell type http://bio-bigdata.hrbmu.edu.cn/CellMarker/ 13607 7219 65981
ChEA TF Targets 2022 gene transcription factor binding site profile http://amp.pharm.mssm.edu/Enrichr/ 17962 757 917047
ChEA TF Targets transcription factor gene http://amp.pharm.mssm.edu/Enrichr/ 21224 199 386776
ClinVar gene phenotype https://www.ncbi.nlm.nih.gov/clinvar/ 2458 3291 3638
LINCS L1000 CMAP Signatures of Diff Expressed Genes chemical perturbation gene https://portals.broadinstitute.org/cmap/ 12148 6100 1201897
CORUM gene protein complex https://mips.helmholtz-muenchen.de/corum/ 2799 2066 9015
COSMIC CNV gene cell line https://cancer.sanger.ac.uk/cosmic/ 19757 950 102249
COSMIC Mutations gene cell line https://cancer.sanger.ac.uk/cosmic/ 17850 1026 746376
CTD Chemical gene chemical http://ctdbase.org/ 11125 9516 124344
CTD Disease gene disease http://ctdbase.org/ 17255 5218 888519
dbGAP gene trait https://www.ncbi.nlm.nih.gov/gap 5668 510 12769
DeepCoverMOA small molecule perturbation gene http://wren.hms.harvard.edu/DeepCoverMOA/# 7750 874 173748
DepMap Gene Dependency gene cell line https://depmap.org/portal/home/#/ 15946 1095 697098
DEPOD phosphatase gene http://www.depod.bioss.uni-freiburg.de/ 293 112 819
DrugBank gene small molecule https://www.drugbank.ca/ 2368 4928 15261
ENCODE Histone Modification gene histone modification site profile https://www.encodeproject.org/ 22007 435 4454173
ENCODE TF Binding transcription factor binding site profile gene https://www.encodeproject.org/ 22845 1679 8803973
ENCODE TF Targets transcription factor gene https://www.encodeproject.org/ 22452 181 1655383
Roadmap Epigenomics DNA Methylation gene cell type or tissue http://www.roadmapepigenomics.org/ 13691 24 49516
Roadmap Epigenomics Histone Modification gene histone modification site profile http://www.roadmapepigenomics.org/ 21032 383 1201230
Roadmap Epigenomics Gene Expression gene cell type or tissue http://www.roadmapepigenomics.org/ 12824 57 109318
GAD Cell Line gene disease https://geneticassociationdb.nih.gov/ 10702 12778 75029
GAD High Level gene disease https://geneticassociationdb.nih.gov/ 8016 18 28200
GDSC gene cell line https://www.cancerrxgene.org/ 11704 624 280242
GeneRIF gene biological term ftp://ftp.ncbi.nih.gov/gene/GeneRIF/ 15201 91041 2549276
GeneSigDB gene PubMedID https://pubmed.ncbi.nlm.nih.gov/22110038/ 19509 3515 416256
GEO Chem Perturbation chemical perturbation gene https://www.ncbi.nlm.nih.gov/geo/ 21336 415 318530
GEO Disease Perturbation disease perturbation gene https://www.ncbi.nlm.nih.gov/geo/ 18516 233 139800
GEO Gene Perturbation gene perturbation gene https://www.ncbi.nlm.nih.gov/geo/ 22020 738 367922
GEO Kinase Perturbation kinase perturbation gene https://www.ncbi.nlm.nih.gov/geo/ 19789 285 171000
GEO TF Perturbation transcription factor perturbation gene https://www.ncbi.nlm.nih.gov/geo/ 19279 154 151898
GEO Virus Perturbation virus perturbation gene https://www.ncbi.nlm.nih.gov/geo/ 19779 366 222682
GlyGen glycan gene https://glygen.org 2231 1910 20486
GO Bio Process 2023 gene biological process http://geneontology.org/ 14811 12318 198050
GO Cellular Component 2023 gene cellular component http://geneontology.org/ 11089 926 41883
GO Molecular Func 2023 gene molecular function http://geneontology.org/ 12478 3851 50339
GTEx Aging Signatures gene tissue sample https://gtexportal.org/home/ 16047 135 67500
GTEx eQTL gene SNP https://gtexportal.org/home/ 149 7815 149
GTEx Tissue Sample gene tissue sample https://gtexportal.org/home/ 19249 2918 8421702
GTEx Tissue 2023 gene tissue https://gtexportal.org/home/ 17369 53 108000
Guide To Pharm Chem gene ligand (chemical) http://www.guidetopharmacology.org/ 899 4894 9380
Guide To Pharm Protein gene ligand (protein) http://www.guidetopharmacology.org/ 187 211 410
GWAS Catalog gene phenotype http://www.ebi.ac.uk/gwas/home 4356 1007 8255
GWASdb Disease gene disease http://jjwanglab.org/gwasdb 11804 585 217330
GWASdb Phenotype gene phenotype http://jjwanglab.org/gwasdb 12487 822 274574
Heiser gene cell line https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-181/ 15144 56 196872
HMDB gene metabolite http://www.hmdb.ca/ 5326 22137 845725
HPA Cell Lines gene cell line http://www.proteinatlas.org/ 15372 43 102943
HPA Tissue Samples gene tissue sample http://www.proteinatlas.org/ 16658 121 303282
HPA Tissues mRNA gene tissue http://www.proteinatlas.org/ 17426 31 81092
HPA Tissue Protein gene tissue http://www.proteinatlas.org/ 15706 44 138585
HPM gene cell type or tissue http://www.humanproteomemap.org/ 4362 4 4362
HPO gene phenotype https://hpo.jax.org/app/ 3158 6842 304995
Hub Proteins gene hub protein http://amp.pharm.mssm.edu/X2K/ 9362 289 58327
HuGE Navigator gene phenotype https://phgkb.cdc.gov/PHGKB/hNHome.actionn 12055 2715 141799
HumanCYC Pathways gene pathway https://humancyc.org/ 932 286 1839
InterPro gene protein domain http://www.ebi.ac.uk/interpro/ 18002 11015 62614
JASPAR PWMs transcription factor gene http://jaspar.genereg.net/ 21375 111 148069
COMPARTMENTS Curated gene cellular component https://compartments.jensenlab.org/Search 16736 1463 328753
COMPARTMENTS Expts gene cellular component https://compartments.jensenlab.org/Search 6495 59 91061
COMPARTMENTS Text Mining gene cellular component https://compartments.jensenlab.org/Search 14375 2081 546634
DISEASES Curated gene disease https://diseases.jensenlab.org/Search 2252 770 18144
DISEASES Expts gene disease https://diseases.jensenlab.org/Search 4055 350 35164
DISEASES Text Mining gene disease https://diseases.jensenlab.org/Search 15309 4628 832622
TISSUES Curated gene tissue https://tissues.jensenlab.org/Search 16215 643 357465
TISSUES Expts gene tissue https://tissues.jensenlab.org/Searchh 15505 243 274154
TISSUES TextMining gene tissue https://tissues.jensenlab.org/Search 16184 4187 1836577
KEA kinase gene http://amp.pharm.mssm.edu/X2K/ 3406 457 12161
KEGG gene pathway https://www.genome.jp/kegg/ 3947 200 9324
Kinase Library kinase gene https://kinase-library.phosphosite.org/sitee 5046 303 30299
LINCS KiNativ gene chemical bioactivity profile http://lincs.hms.harvard.edu/about/approach/assays/ 102 23 149
LINCS KinomeScan gene small molecule http://lincs.hms.harvard.edu/kinomescan// 277 71 2057
Klijn CNV gene cell line https://www.nature.com/articles/nbt.3080 24922 668 2495888
Klijn mRNA gene cell line https://www.nature.com/articles/nbt.3080 13944 650 1357992
Klijn Mutations gene cell line https://www.nature.com/articles/nbt.3080 14367 676 133818
KnockTF transcription factor perturbation gene http://www.licpathway.net/KnockTF/index.html 17963 566 108820
IMPC Knockout gene phenotype https://mousephenotype.org 6763 667 36451
LINCS L1000 CMAP Chem Pert Consensus Signatures gene chemical perturbation https://clue.io/ 12126 23913 5086167
LINCS L1000 CRISPR gene gene perturbation https://clue.io/ 9551 5049 2524500
LINCS L1000 CMAP Signatures of Diff Expressed Genes chemical perturbation gene https://clue.io/ 8347 31028 4189677
LOCATE Curated Protein gene cellular component http://locate.imb.uq.edu.au/ 9639 78 79181
LOCATE Predicted Protein gene cellular component http://locate.imb.uq.edu.au// 19747 24 154700
MPO Phenotype gene phenotype http://www.informatics.jax.org/phenotypes.shtml 7798 8579 466673
MPO Mouse Phenotype 2023 gene phenotype http://www.informatics.jax.org/phenotypes.shtml 12894 10234 252920
MiRTarBase microRNA gene http://mirtarbase.mbc.nctu.edu.tw/php/index.php 12086 596 37415
MotifMap transcription factor gene http://motifmap-rna.ics.uci.edu/ 20432 331 158860
MoTrPAC gene tissue sample https://www.motrpac.org 12426 142 95052
MSigDB Comp Signatures gene co-expressed gene http://software.broadinstitute.org/gsea/msigdb/index.jsp 4869 356 41327
MSigDB Oncogenic Signatures gene perturbation gene http://software.broadinstitute.org/gsea/msigdb/index.jsp 10765 90 29967
MW Metabolites gene metabolite https://www.metabolomicsworkbench.org/ 1068 731 5042
OMIM gene phenotype http://www.omim.org/ 4553 5540 6666
PANTHER gene pathway http://pantherdb.org/ 1962 145 4255
Pathway Commons gene interacting protein http://www.pathwaycommons.org/ 15747 15747 3527164
WikiPathways PFOCR gene pathway https://www.wikipathways.org/index.php/WikiPathways 13173 35464 307416
PhosphoSitePlus Kinase kinase gene https://www.phosphosite.org/homeAction.action 2447 359 6013
PhosphoSitePlus Disease gene disease https://www.phosphosite.org/homeAction.action 212 140 356
Phosphosite Textmining gene biological term https://www.phosphosite.org/homeAction.action 2857 881 159580
PID Pathways gene pathway https://github.com/NCIP/pathway-interaction-database/tree/master/download 2510 223 8027
Proteomics DB gene cell type or tissue https://www.proteomicsdb.org/ 2776 53 21921
Reactome gene pathway https://reactome.org/ 7535 1638 83680
Sanger Dep Map gene cell line https://depmap.sanger.ac.uk/ 8230 949 189800
SILAC Drug Perturbation drug perturbation gene https://www.phosphosite.org/homeAction.action 2770 23 5808
SILAC Gene Perturbation gene perturbation gene https://www.phosphosite.org/homeAction.action 203 10 840
SILAC Ligand Perturbation ligand (protein) perturbation gene https://www.phosphosite.org/homeAction.action 2022 9 5439
Tabula Sapiens gene cell https://tabula-sapiens-portal.ds.czbiohub.org/ 8184 469 46900
TargetScan Conserved microRNA gene http://www.targetscan.org/vert_72/ 14923 1537 513997
TargetScan Nonconserved microRNA gene http://www.targetscan.org/vert_72/ 18048 1539 627985
TCGA gene tissue sample https://cancergenome.nih.gov/ 19794 5904 4367061
VirusMINT Virus gene virus https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686573/ 706 68 1036
VirusMINT Viral Protein gene viral protein https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686573/ 706 185 1140
WikiPathways Pathways gene pathway https://www.wikipathways.org/index.php/WikiPathways 6093 427 22242