Additional Data

L. Yang et al. Transcription factor family-specific DNA shape readout revealed by quantitative specificity models.
Mol. Syst. Biol. in press (2017)
Supplementary Information

This page provides download links for all the trained models related to the paper, as well as the preprocessed M-word scores and encoded features for reproducing the results. Each MLR model is the average of 10 models learned from 10-fold cross validation. PSSMs were information content calculated based on top 200 M-words for each TF.



Model Link
1mer Download
1mer+shape Download
1mer+shape+3merE2 Download
1mer+2mer+3mer Download
1mer+2merNoE2+3merNoE2 Download
3mer Download
1mer+shapei Download
shape (first&second order) Download
shape-shapei Download
shape (first order) Download
PSSM (sequence) Download
PSSM (shape) Download

M-word scores: Download
Each file contains three columns. The first column are the M-words. The second column are the relative affinity scores for the correspoinding M-words. And the third column are M-word counts.

Encoded features: Download
In each of the feature files, the first column is log2(M-word score). And the second column is constant 1. The rest of the columns are the encoded features. Naming of the features is as the following:
1mer features: *.10000000000
First-order MGW features: *.00010000000
First-order Roll features: *.00001000000
First-order ProT features: *.00000100000
First-order HelT features: *.00000010000
Second-order MGW features: *.00000001000
Second-order Roll features: *.00000000100
Second-order ProT features: *.00000000010
Second-order HelT features: *.00000000001
1mer+shape features: *.10011111111
Standard deviations used for normalizing the shape features: *.scale

February 6, 2017
Our new Mol. Syst. Biol. paper provides systematic analysis of DNA shape readout for many protein families. Congrats, Lin!

November 30, 2016
Our new Nature paper with the Leibniz Institute on Aging reveals role of Hoxa9 in muscle stem cell aging.

November 8, 2016
Our recent Dror et al. Genome Res. paper received a RECOMB/ISCB Top-10 Paper Award in regulatory and systems genomics in 2015/16.

August 31, 2016
Carolina defended her Ph.D. thesis with flying colors. Congratulations, Carolina!

August 18, 2016
Our new paper proves the impact of DNA shape on in vivo TF binding based on 400 human ChIP-seq datasets.

August 16, 2016
Remo was promoted to Full Professor of Biological Sciences at USC. Fight on!

July 14, 2016
Remo was elected Head of Computational Biology and Bioinformatics at USC. Fight on!

June 6, 2016
Lin defended his Ph.D. thesis with flying colors. Congratulations, Lin!

May 4, 2016
Tsu-Pei received a competitive Enhancement Fellowship from the USC Graduate School. Congratulations, Tsu-Pei!

May 3, 2016
Lin received the highest honor for a USC graduate student, the PhD Achievement Award. Congratulations, Lin!

May 3, 2016
Remo was introduced as the incoming Vice Chair of the Department of Biological Sciences and Director of Biological Sciences Studies.

April 20, 2016
Remo presented our recent Zhou et al. PNAS paper as one of the few selected Highlights at the recent RECOMB conference.

April 19, 2016
Carolina received the Harrison M. Kurtz Award and Tsu-Pei the William E. Trusten Award. Congrats, Carolina and Tsu-Pei!.

April 6, 2016
Remo received the USC Mentoring award in the category mentoring of graduate students. Best award ever!

March 16, 2016
Remo received the ACS OpenEye Outstanding Junior Faculty Award in Computational Chemistry at the American Chemical Society National Meeting.

January 28. 2016
Remo received Tenure at USC and was promoted to Associate Professor. Fight on!

November 18, 2015
Our recent Abe et al. Cell and Zhou et al. PNAS papers were voted as RECOMB/ISCB Top Papers in regulatory and systems genomics in 2014/15.

Recent news

August 21-25, 2016
Symposium on Modeling Water and Solvation in Biochemistry: Developments and Applications, American Chemical Society National Meeting, Philadelphia, PA

July 5-8, 2016
Meeting on Measuring and Modeling Quantitative Sequence-Function Relationships, Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, NY

April 17-21, 2016
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March 23, 2016
Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany

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CSHL Meeting on Systems Biology: Global Regulation of Gene Expression, Cold Spring Harbor Laboratory, NY

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February 5-7, 2016
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January 31- February 5, 2016
Epigenomics 2016 Meeting, Rio Mar, Puerto Rico

January 19, 2016
Bioinformatics and Computational Biology Research Center, Cedars-Sinai Medical Center, Los Angeles, CA

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