motifAnnotations: Annotations of Motifs to TFs

In aertslab/RcisTarget: RcisTarget Identify transcription factor binding motifs enriched on a list of genes or genomic regions

Annotations of Motifs to TFs

Description

• motifAnnotations_hgnc: Annotations to HUMAN transcription factors for the rankings using motif collection version 10. Source: motifs-v10nr_clust-nr.hgnc-m0.001-o0.0.tbl

• motifAnnotations_mgi: Contains the annotations to MOUSE transcription factors for the rankings using motif collection version 10. Source: motifs-v10nr_clust-nr.mgi-m0.001-o0.0.tbl

• motifAnnotations_dmel: Contains the annotations to FLY transcription factors for the rankings using motif collection version 10. Source: motifs-v10nr_clust-nr.flybase-m0.001-o0.0.tbl

Previous versions:

Annotations for motif collection version 9 ('mc9nr').

• Human: motifAnnotations_hgnc_v9 (motifs-v9-nr.hgnc-m0.001-o0.0.tbl)

• Mouse: motifAnnotations_mgi_v9 (motifs-v9-nr.mgi-m0.001-o0.0.tbl)

• Fly: motifAnnotations_dmel_v9 (motifs-v9-nr.flybase-m0.001-o0.0.tbl)

Annotations for motif collection version 8 ('mc8nr'). - Deprecated: Will be removed in upcoming versions of the package

• 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. The original files can be downloaded from https://resources.aertslab.org/cistarget/motif2tf/ 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

aertslab/RcisTarget documentation built on March 7, 2024, 11:21 p.m.