motifAnnotations: Annotations of Motifs to TFs

In RcisTarget: RcisTarget: Identify transcription factor binding motifs enriched on a gene list

Description

• motifAnnotations_hgnc: Annotations to HUMAN transcription factors for the rankings using motif collection version 9 ('mc9nr', 24453 motifs).

  Source: motifs-v9-nr.hgnc-m0.001-o0.0.tbl

• motifAnnotations_mgi: Contains the annotations to MOUSE transcription factors for the rankings using motif collection version 9 ('mc9nr', 24453 motifs).

  Source: motifs-v9-nr.mgi-m0.001-o0.0.tbl

• motifAnnotations_dmel: Contains the annotations to FLY transcription factors for the rankings using motif collection version 9 ('mc9nr', 24453 motifs).

  Source: motifs-v9-nr.flybase-m0.001-o0.0.tbl

• Previous versions: Annotations for motif collection version 8 ('mc8nr').

  • Human: motifAnnotations_hgnc_v8 (motifs-v8-nr.hgnc-m0.001-o0.0.tbl)

  • Mouse: motifAnnotations_mgi_v8 (motifs-v8-nr.mgi-m0.001-o0.0.tbl)

  • Fly: motifAnnotations_dmel_v8 (motifs-v8-nr.flybase-m0.001-o0.0.tbl)

These objects are meant to be provided to RcisTarget without modification, but it can also be explored by the user to obtain further information about the motifs. Columns:

• motif: Motif ID.

• TF: Transcription factor (or inferred gene).

• directAnnotation, inferred_Orthology, inferred_MotifSimil: Boolean values indicating whether the motif is annotated to the TF in the source database ("directAnnotation"), or whether it was inferred by orthology ("inferred_Orthology") or motif similarity ("inferred_MotifSimil").

• Description: Description of the source of the annotation.

• annotationSource: Source of the annotation formatted as factor (e.g. for subsetting). Levels: directAnnotation, inferredBy_Orthology, inferredBy_MotifSimilarity, inferredBy_MotifSimilarity_n_Orthology.

Details

Documentation for the data

See Also

importAnnotations, RcisTarget

RcisTarget documentation built on Nov. 8, 2020, 6:57 p.m.