Table 1.
Comparison of TFmotifView features to other known motif search tools
| Tools | TFmotifView | AME (MEME suite) | CENTRIMO (MEME suite) | i-cisTarget | Pscan-ChIP | HOMER | JASPAR database |
|---|---|---|---|---|---|---|---|
| Reference | This article | 13 | 16 | 14 | 15 | 12 | 8 |
| Online web server | YES | YES | YES | YES | YES | NO (command line) | NA |
| Input format | BED regions | FASTA sequences | FASTA sequences (same length) | BED regions | BED regions (150bp) | BED regions (200bp or all) | NA |
| Genome | hg38, hg19 mm10, mm9 | No genome required | No genome required | hg19 mm9 dm3,dm6 daphnia | hg38, hg19, hg18 mm10, mm9 | Available locally | hg38, hg19 mm10 dm6, ce10 danRer11 araTha1 sacCer3 |
| Motif database | JASPAR or provided | JASPAR, others or provided | JASPAR or others | Several | JASPAR, TRANSFAC or provided | Custom | JASPAR |
| Motif score threshold | Dynamic P-value using information content (most below 10−3) or custom | hit threshold 0.25 | 5 bits - likelyhood ratio 32 (score does not affect results) | No threshold (motifs are used to define i-cisTarget regulatory regions) | No threshold (comparing best score in input regions vs. background regions) | P-value 0.05 | NA |
| Uses control regions | YES (sampled from mappable, not blacklisted regions or provided) | YES (shuffled input FASTA sequences) | NO | NO | YES (sampled from ENCODE DNase regions) | YES (large number sampled from regions within 50Kb of gene TSS or provided) | NA |
| Corrects for G+C content | YES | YES (preserves 2mers) | NO | NO | NO (allows from mixed or promoter regions) | YES (by G+C or CpG) | NA |
| Table of motif enrichment | YES | YES | NO | YES | YES | YES | NA |
| (strategy does not allow to provide the number of regions having a motif) | |||||||
| Measure of enrichment | Hyper-geometric P-value | Fisher's exact adjusted P-value | Binomial e-value | Normalized enrichment score | T-test P-value | Binomial P-value | NA |
| Graphical representation of motif enrichment | YES (enrichment vs foldchange for all motifs) | NO | NO | YES (AUC per motif) | NO | NO | NA |
| Genomic view | Custom + UCSC genome browser (choice of motif and threshold) | NO | NO | UCSC genome browser for predicted regions | Link to JASPAR track | NO | UCSC genome browser (all motifs at default threshold) |
| Enrichment at region center | YES | NO | YES | NO | YES | Script available | NA |