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= The PWMs Repository =
''' This page lists the available PWMs and its corresponding data.'''

== Directions for adding PWM's data ==

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This page lists the details and data of the available PWMs and their corresponding data. The PWMs can be added to this page in PWM format or as list of binding peptides per domain. 
When you add a new data set, please consider adding the following information.
1- The source of the dataset: the published article, the database or the lab (if unpublished).
2- The domain data: the name of the domains family, the domain names and all available data about them.
3- The PWM files: can either be in PWM format or list or peptides per domain.
4- Positive peptides dataset: list of experimentally confirmed binding peptide per domain.
5- Negative peptides dataset (experimental): list of experimentally confirmed peptide that cannot bind to each domain.     
6- Negative peptides dataset (computational): list of peptide used as negative dataset per domain but not experimentally confirmed (e.g. random genomic peptides). 
7- The sequence logos of each PWM.
8- Add description and statistics to your dataset.
9- Add comments about any missing prices of information of your added dataset.

When adding new dataset, please name it as following "Domain Name (Organism)" e.g. WW Domain (Human).
     
}}}

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== SH3 Domain (Human) ==

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Description and data sources:

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- [[attachment:Domains.zip|Domains Information (Names, Sequences, Proteins ID ...).]]

- [[attachment:SH3-PWMs.zip|PWM files.]]

- Positive peptides dataset. 

- [[attachment:SH3-Nig-Peps-Exp.zip|Negative peptides dataset (experimental).]]

- [[attachment:SH3-Nig-Peps-Comp.zip|Negative peptides dataset (Computational).]]

- [[attachment:SH3-Logos.PDF|Sequence logos.]]

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== SH2 Domain (Human) ==

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Description and data sources:
- Data set of human SH2 Domain published in http://www.nature.com/ng/journal/v46/n12/full/ng.3138.html.
- The data obtained from the supplementary material of the paper and it descries the domains and the positive and negative peptide datasets used for training the statistical models used in this work. The peptide datasets are mainly obtained from 5 published SH2 studies (cited in the article).
}}}

- [[attachment:SH2-Domain-Peptides.zip|Domains and peptides Information.]]

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== Phosphokinase-Binding Domains (Human) ==
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Description and data sources:

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- Domains Information (Names, Sequences, Proteins ID ...).

- [[attachment:MIMP-PWMs.zip|PWM files.]]

- Positive peptides dataset. 

- Negative peptides dataset (experimental).

- Negative peptides dataset (Computational).

- [[attachment:MIMP-logos.zip|Sequence logos.]]

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== Transcription Factors (Human) ==

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Description and data sources: 
- Data set of human transcription factor binding sites published in http://www.ncbi.nlm.nih.gov/pubmed/25215497.
- Data obtained from CIS-BP database (http://cisbp.ccbr.utoronto.ca/) on October 24, 2014. The data contains >4000 PWM and all the corresponding transcription factor information and logos.
- Please note that: many PWMs in this dataset are not completely available due to licence issues.  


}}}

- [[attachment:Human-TF-All.zip|All Information (PWMs, Logos, TF Data, Scores...).]]