Promoter AI

Professional data source

This is a Professional data source and is not available freely. Please contact annotation_support@illumina.com if you would like to obtain it.

Overview

Promoter AI is one of the many AI-based annotation data from Illumina. It calculates score of possible variant on the promoter region. A promoter region is described as 500nt upstream and downstream of a transcript's transcription starting site (TSS). Each annotation will show score of the variant and which transcript and gene the promoter region corresponds to. The gene and transcript data is generated using gene annotation data from GENCODE Release 39 (corresponds to Ensembl release 105).

Transcript and Gene IDs from Promoter-AI

Illumina Connected Annotation uses its own transcript and gene cache data for reporting transcript annotation and can be different from the one reported in Promoter AI (based on GENCODE Release 39). This can result in some differences in the transcript ID and gene ID shown in the annotation result.

Parsing

TSV File

gene_id chrom   pos ref alt strand  gene    transcript_id   tss_pos strand_adj_dist_tss score_x score_y score
ENSG00000181404 chr9    73364   G   A   -1  WASHC1  ENST00000642633.1   73864   500 -0.0032 -0.0298 -0.0165
ENSG00000181404 chr9    73364   G   C   -1  WASHC1  ENST00000642633.1   73864   500 -0.0372 -0.052000000000000005   -0.0446
ENSG00000181404 chr9    73364   G   T   -1  WASHC1  ENST00000642633.1   73864   500 0.0202  -0.0315 -0.0056500000000000005
ENSG00000181404 chr9    73365   G   A   -1  WASHC1  ENST00000642633.1   73864   499 -0.015  -0.0643 -0.03965
ENSG00000181404 chr9    73365   G   C   -1  WASHC1  ENST00000642633.1   73864   499 0.0285  -0.0035 0.0125
ENSG00000181404 chr9    73365   G   T   -1  WASHC1  ENST00000642633.1   73864   499 -0.0095 -0.0352 -0.022350000000000002
ENSG00000181404 chr9    73366   G   A   -1  WASHC1  ENST00000642633.1   73864   498 0.0068  -0.0565 -0.02485
ENSG00000181404 chr9    73366   G   C   -1  WASHC1  ENST00000642633.1   73864   498 0.0596  0.0854  0.07250000000000001
ENSG00000181404 chr9    73366   G   T   -1  WASHC1  ENST00000642633.1   73864   498 -0.0086 -0.0009 -0.00475
ENSG00000181404 chr9    73367   C   A   -1  WASHC1  ENST00000642633.1   73864   497 0.0091  -0.0068 0.0011500000000000004
...

From the file, we extract column gene_id, transcript_id, strand, strand_adj_dist_tss, and score.

JSON Output

"promoterAI": [
    {
      "strand": 1,
      "distanceFromTss": -292,
      "geneId": "ENSG00000274391",
      "transcriptId": "ENST00000618007.5",
      "score": 0.032
    }
]

Field	Type	Notes
strand	int	Strand location of the transcript
distanceFromTss	int	Number of nucleotides calculated from TSS of teh corresponding transcript
geneId	string	Gene ID
transcriptId	string	Transcript ID (Ensembl)
score	decimal	Calculated Promoter AI score

Interpreting Score

The score annotation from Promoter AI has range between -1 and 1. Positive score shows that the corresponding variant has over expression effect to the target gene while Negative score has under expression effect to the target gene. If the score is between -0.05 and 0.05 it doesn't have any efefct to the target gene.