Gene Metadata

The genes of tkoi_net that can seed an analysis, with their Ensembl IDs and network degree. run_tkoi maps gene_name to ensembl, and draws degree-matched replacement genes for the permutation null from this table.

Usage

genes

Format

A data frame (data.table) with 17,569 rows and 5 columns:

id

Character. Node ID of the gene in tkoi_net.

identifier

Integer. NCBI Entrez Gene ID.

ensembl

Character. Ensembl gene ID. A few genes have no Ensembl ID (empty string), and a few Ensembl IDs map to two genes.

name

Character. Gene symbol.

degree

Integer. Degree of the gene node in tkoi_net.

Details

This dataset is essential for integrating gene-level information with biological networks and functional studies.

Examples

data(genes)
head(genes)
#>                                                id identifier         ensembl
#>                                            <char>      <int>          <char>
#> 1:   4:c77f6410-bc08-43ba-a172-0503ab1c93db:16050     389611 ENSG00000233132
#> 2:   4:c77f6410-bc08-43ba-a172-0503ab1c93db:17633     389630 ENSG00000230045
#> 3:   4:c77f6410-bc08-43ba-a172-0503ab1c93db:47899     151507 ENSG00000293137
#> 4: 4:c77f6410-bc08-43ba-a172-0503ab1c93db:2490276          1 ENSG00000121410
#> 5: 4:c77f6410-bc08-43ba-a172-0503ab1c93db:2490277          2 ENSG00000175899
#> 6: 4:c77f6410-bc08-43ba-a172-0503ab1c93db:2490278          9 ENSG00000171428
#>        name degree
#>      <char>  <int>
#> 1:  FAM90A3      8
#> 2: FAM90A15     26
#> 3:    MSL3B    105
#> 4:     A1BG    129
#> 5:      A2M    566
#> 6:     NAT1    239