Semyonk@dote.ru: Created page with "Prediction of TF-binding sites of given TF in whole genome or in given chromosome fragment or in ChIP-Seq dataset. Sites are predicted by different Position Weight Matrix (PWM..."

2019-05-02T15:33:42Z

Created page with "Prediction of TF-binding sites of given TF in whole genome or in given chromosome fragment or in ChIP-Seq dataset. Sites are predicted by different Position Weight Matrix (PWM..."

New page

Prediction of TF-binding sites of given TF in whole genome or in given chromosome fragment or in ChIP-Seq dataset. Sites are predicted by different Position Weight Matrix (PWM) methods.
== Description ==
The following 6 PWM methods (models) were available:
# Given HOCOMOCO site models (Kulakovskiy et al, 2016). These models are available in HOCOMOCO database. They are located at "databases/HOCOMOCO v11/Data/PWM_HUMAN_mono_pval=0.0001”
# MATCH models (Kel et al, 2003);
# Additive IPS (Individual Probability Score) models, or briefly, IPS models (Volkova et al, 2018);
# Multiplicative IPS models. These models can be reduced to equivalent additive IPS models by taking logarithms of matrix elements;
# Common additive models;
# Common multiplicative models.

For determination of common additive and multiplicative models let’s matrix MAT = (m<sub>ij</sub>), i={A,C,G,T}, denotes the given frequency matrix, j=1,...,l and l denotes the length of sites. For this analysis we used HOCOMOCO frequency matrices available in HOCOMOCO database (Kulakovskiy et al, 2016). These matrices They are located at “"databases/HOCOMOCO v11/Data/PCM_HUMAN_mono/”.
To test an arbitrary DNA fragment S=(s<sub>1</sub>,...,s<sub>l</sub>), the common additive score x is determined using a standard way:
<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">x = Σj=1,...,l score(j),</div>
where the score(j), j=1,…,l, are determined as follows:
<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">score(j) = {m<sub>Aj</sub>, if s<sub>j</sub>=A; m<sub>Cj</sub>, if s<sub>j</sub>=C; m<sub>Gj</sub>, if s<sub>j</sub>=G; m<sub>Tj</sub>, if s<sub>j</sub>=T;}, j=1,…,l</div>
The common multiplicative score y is determined by formula:
<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">y = ∏<sub>j=1,...,l</sub> score(j).</div>
If the the calculated score (x or y) exceeds the pre-specified threshold, then the tested DNA fragment S is declared as the predicted site.
It is important to note that common multiplicative model can be converted to equivalent additive model by taking logarithms of matrix elements, i.e.
<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">y = Σ<sub>j</sub>=1,...,l score*(j),</div>
where the values score*(j), j=1,…,l, are determined as follows:
<div class="center" style="width: auto; margin-left: auto; margin-right: auto;">score*(j) = {ln(m<sub>Aj</sub>), if s<sub>j</sub>=A; ln(m<sub>Cj</sub>), if s<sub>j</sub>=C; ln(m<sub>Gj</sub>), if s<sub>j</sub>=G; ln(m<sub>Tj</sub>) if s<sub>j</sub>=T}.</div>

=== References ===

Kulakovskiy,I.V., Vorontsov,I.E., Yevshin,I.S., Soboleva,A.V., Kasianov,A.S., Ashoor,H., Ba-Alawi,W., Bajic,V.B., Medvedeva,Y.A., Kolpakov,F.A. et al. (2016) HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. Nucleic Acids Res., 44, D116–D125.

Kel, A.E., Gobling, E., Reuter, I., Cheremushkin, E., Kel-Margoulis, O.V. and Wingender, E. (2003) MATCHTM: a tool for searching transcription factor binding sites in DNA sequences, Nucleic Acids Res., 31, p.3576-3579.

Volkova OA, Kondrakhin YV, Kashapov TA, Sharipov RN. Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features. J Bioinform Comput Biol. 2018 Apr;16(2):1840013. doi: 10.1142/S0219720018400139.

== Analysis Parameters: ==
* '''Sequence set type''' – Select type of sequences;
** '''Available sequence types''': 1) Whole genome 2) Chromosome fragment 3) ChIP-Seq peaks from given track
* '''Sequences collection''' – Select a source of nucleotide sequences
** '''Sequences source''' – Select database to get sequences from or 'Custom' to specify sequences location manually
** '''Sequence collection''' – Specify path to folder containing sequences if 'Custom' sequences source is selected
* If '''Sequence set type''' = Chromosome fragment
** '''Chromosome name''' – Select chromosome name
** '''Start position''' – Type start position of chromosome fragment
** '''Finish position''' – Type finish position of chromosome fragment
* If '''Sequence set type''' = ChIP-Seq peaks from given track
** '''Path to track''' – Select Path to track with ChIP-Seq dataset; For example, track from GTRD database can be selected, i.e. Path to track = databases/GTRD/Data/peaks/gem/PEAKS033057
* '''Site name''' – type name of predicted sites
* '''Prediction models''' – Define prediction models. User can define several prediction models.
** '''modelName''' – Type model name
** '''siteType''' – Select site type;
*** '''Available site types:''' 1) Given site model 2) IPS model 3) Multiplicative IPS model 4) Common additive model 5) Common multiplicative model 6) MATCH model
** If '''siteType''' = Given site model
*** '''modelPath''' – Input path to given site prediction model. In particular, user can select given site model from HOCOMOCO database, such as "databases/HOCOMOCO v11/Data/PWM_HUMAN_mono_pval=0.0001/CEBPA_HUMAN.H11MO.0.A"
** If '''siteType''' ≠ Given site model
*** '''matrixPath''' - Input path to given frequency matrix . In particular, user can select given frequency matrix from HOCOMOCO database, such as "databases/HOCOMOCO v11/Data/PCM_HUMAN_mono/CEBPA_HUMAN.H11MO.0.A"
*** '''threshold''' - Type threshold
* '''The output track name''' – Type the output track name
* '''Path to output folder''' – Path to output fold

Site prediction - Revision history

Semyonk@dote.ru: Created page with "Prediction of TF-binding sites of given TF in whole genome or in given chromosome fragment or in ChIP-Seq dataset. Sites are predicted by different Position Weight Matrix (PWM..."