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Labeling this number of sequences as 'positive' was found by AME to be optimal (or your primary sequence file contains this number of sequences and you also provided a control sequence file). The sequences were chosen as described above under "Labeling positives".

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Labeling this number of sequences as 'negative' was found by AME to be optimal (or you provided a control sequence file containing this number of sequences). The sequences are those remaining after the 'positive' sequences were chosen as described above under "Labeling positives".

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The number (percentage) of sequences labeled as 'positive' (Pos) and classified as 'positive' (TP),

%TP = 100 * TP/Pos.

Labeling of sequences as 'positive' is described in the help bubble for "Pos".
Classification is described above under "Classifying positives".

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The number (percentage) of sequences labeled as 'negative' (Neg) but classified as 'positive' (FP),

%FP = 100 * FP/Neg.

Labeling of sequences as 'negative' is described in the help bubble for "Neg".
Classification is described above under "Classifying positives".

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The (optimal) score threshold for **labeling** sequences as 'positive' determined by AME.
(See the note about "Labeling positives" in the section above.)

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The (optimal) score threshold for **classifying** sequences as 'positive' determined by AME (or provided by
you using `--hit-odds-fraction`

or `--fasta-threshold`

).

By default, the true positive and false positive sequences are those with sequence motif scores ≥ the value shown.

If you specified `--poslist pwm`

, then the true positive and false positive sequences are those with
FASTA scores ≤ the value shown.

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The value of Pearson's correlation coefficient (ρ).
It varies between -1 and +1.
High values of ρ indicate strong correlation between the
sequence motif scores and the sequence FASTA scores.
Note that positive ρ means that sequence motif scores go **up**
when sequence FASTA scores go **down**.
The *p*-value of this method is the probability that ρ is at least as
large as the observed value assuming there is no relation between the scores.

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The value of Spearman's rank correlation coefficient (ρ).
It varies between -1 and +1.
High values of ρ indicate strong correlation between the
sequence motif score ranks and the sequence FASTA score ranks.
Note that positive ρ means that sequence motif scores go **up**
when sequence FASTA scores go **down**.
The *p*-value of this method is the probability that ρ is at least as
large as the observed value assuming there is no relation between the scores.

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The value of the mean squared error of the linear regression of X vs Y.

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The slope of the regression line: Y = mX + b.

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The Y-intercept of the regression line: Y = mX + b.

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For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org.

If you use AME in your research, please cite the following paper:

Robert McLeay and Timothy L. Bailey,
"Motif Enrichment Analysis: A unified framework and method evaluation",
*BMC Bioinformatics*, **11**:165, 2010, doi:10.1186/1471-2105-11-165.
[full text]

Logo | Database | ID | Alt ID | p-value |
E-value |
Pos Thresh | Pos | Neg | TP Thresh | TP (%) | FP (%) | Pearsons's CC (ρ) | Spearman's Rank CC (ρ) | Mean squared error | m | b |
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Database | Source | Motif Count |
---|