Get cCRE Gene links

NOTE: You can also find cCRE-Gene link files to download in cCRE-Gene Links section of https://screen.wenglab.org/downloads

Get Near by genes from given cCREs

Returns 3 nearest by genes for a cCRE by distance.

 query {
  getmaxZScoresQuery(assembly: "grch38", accession: ["EH38E1310345"]) {
    accession
    chromosome   
    start    
    stop
    ccre_group  
    nearestgenes {
      distance
      gene
    }

  }
}

Get linked genes

Returns Intact-HiC linked genes if assay is Intact-HiC, ChIAPET linked genes if assay is RNAPII-ChIAPET or CTCF-ChIAPET, CRISPR linked genes if method is CRISPR and lastly eQTLs genes if method is eQTLs

This data is only available for Human

query {
  linkedGenesQuery(assembly: "grch38", accession: ["EH38E1516972"]) {
      accession  
      p_val
      gene
      geneid
      genetype
      method
      grnaid
      effectsize
      assay
      celltype
      experiment_accession
      tissue
      variantid
      source
      slope
      score
      displayname
    }
}

Get Computational linked genes

Returns linked genes for a cCRE by various methods like ABC_(DNase_only),ABC_(full), EPIraction,GraphRegLR,rE2G_(DNase_only) and rE2G_(extended).

This data is only available for Human

 query {
    ComputationalGeneLinksQuery(accession: ["EH38E1516972"], method: ["ABC_(full)"]){
      genename
      accession
      geneid
      genetype
      method
      celltype
      score
      methodregion
      fileaccession
    }
  }