Binding Queries

• Binding
  • List Binding Genes
  • Binding Histogram
  • List Gene-binding Mapping Files
  • Get Gene-binding Map
• Exons
  • Get Exons
  • Gene Locus
• Bed
  • List Bed
  • Bed Motifs

List Binding Genes

Gets the list of supported binding genes.

Params

type: string,  // ='list-binding'

Return

!Array<{
  fileName: string,
  gene: string,
  description: string，
  chrs: !Array<string>
}>

Binding Histogram

Gets a sampled histogram of the binding data.

Params

type: string,         // ='binding'
fileName: string,     // File name of the binding regulator.
chr: string,          // Chromosome.
xl: ?number,          // Start coordinate of the binding range. If null, use the leftmost coordinate of the track.
xr: ?number,          // End coordinate of the binding range. If null, use the rightmost coordinate of the track.
numSamples: =number,  // Number of samples. If not specified, use the default number.

Return

{
  gene: string,
  chr: string,
  xMin: number,
  xMax: number,
  valueMax: number,
  allValueMax: number,
  values: !Array<{
    x: number, // histogram's x coordinate
    value: number
  }>
}

List Gene-binding Mapping Files

Gets the list of gene-binding mapping files.

Params

type: string,  // ='list-mapping'

Return

fileList: !Array<string>

Get Gene-binding Map

Gets the map of genes and binding file names.

Params

type: string,  // ='mapping'
fileName: string,

Return

mappingName: !Object<string>

Get Exons

Get the full list of exons.

Params

type: string // ='exons'

Return

!Array<{
  name: string,
  name2: string,
  chr: string,
  strand: string, // '+' or '-'
  txStart: number,
  txEnd: number,
  cdsStart: number,
  cdsEnd: number,
  exonRanges: !Array<{
    start: number,
    end: number
  }>
}>

Gene Locus

Searches the exon file for a given gene.

Params

type: string, // ='locus'
gene: string  // Name of the gene to be searched for.

Return

{
  chr: string, // The locus chromosome the gene is at.
  txStart: number,
  txEnd: number
}

List Bed

Gets the info for all uploaded bed tracks.

Params

type: string  // ='list-bed'

Return

!Array<{
  fileName: string,
  bedName: string,
  description: string
}>

Bed Motifs

Gets the motif ranges in bed data.

Params

type: string,            // ='bed'
bedName: string,         // Name of the bed track data.
chr: string,             // Chromosome.
xl: (number|undefined),  // Left coordinate of the query range. If undefined, use the leftmost coordinate of the track.
xr: (number|undefined)   // Right coordinate of the query range. If undefined, use the rightmost coordinate of the track.

Return

The returned motifs will be sorted by first chrStart and then chrEnd. If the number of motifs in the query range exceeds the threshold (currently 200, aggregated motifs will be returned to abstract the motif ranges). Aggregated motif ranges will not have labels.

{
  aggregated: boolean,
  motifs: !Array<{
    chrStart: number,
    chrEnd: number,
    label: (string|undefined)
  }>
}