New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

Overview

We have screened a 41-way vertebrate genomic alignment for structural RNA families. We have identified novel families of human paralogous structural RNAs using the EvoFam family-identification pipeline, which is based on structured regions located by EvoFold. These pages present the resulting identified familes as well as supplementary data sets, such as initial structural RNA predictions, genomic input regions, multiple alignment segments, etc.

The analysis is based on data from the "29 mammals sequencing and analysis consortium" (Lindblad-Toh et al.). See references below.

All genomic coordinates are relative to the Human March 2006 (hg18) assembly.

EvoFam predictions of structural RNA families

EvoFam Main Predictions
Dataset name	Brief description	Browse	Tab format	AMA files
GW	Genome-wide prediction set
UTRP	UTR with paralogs prediction set
GWP	Genome-wide with paralogs prediction set
Note: Examine the EvoFold v.2 and EvoFold paralogs tracks from the "Genes and Gene Prediction Tracks" section of the genome browser for genomic location and structures of the predictions

EvoFam Auxiliary Data Sets
Dataset name	Brief description	Browse	Tab format	AMA files
GW unfiltered	Genome-wide unfiltered prediction set
UTRP unfiltered	UTR with paralogs unfiltered prediction set
GWP unfiltered	Genome-wide with paralogs unfiltered prediction set

Other EvoFam Raw Data Dump (tab format)
	Filtered set (no length filtering)	Filtered set (no GO filtering)
GW set
UTRP set
GWP set

EvoFold predictions of structural RNAs

EvoFold Main Predictions
Prediction sets	link
Input EvoFold set
EvoP scores / p-values
Substitution statistics for input set

EvoFold Auxiliary Data Sets
Input conserved regions
Tiled, conserved input regions
Filtered multiple alignment for each prediction
Benchmark set of 364 known, conserved structural RNAs
Comprehensive set of structural RNA annotations

References

Brian J. Parker, Ida Moltke, Adam Roth, Stefan Washietl, Jiayu Wen, Manolis Kellis, Ronald Breaker, and Jakob Skou Pedersen.
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Research (2011).

Kerstin Lindblad-Toh, Manuel Garber, Or Zuk, Michael F. Lin, Brian J. Parker, Stefan Washietl, Pouya Kheradpour, Jason Ernst, Gregory Jordan, Evan Mauceli, Lucas D. Ward, Craig B. Lowe, Alisha K. Holloway, Michele Clamp, Sante Gnerre, Jessica Alfoldi, Kathryn Beal, Jean Chang, Hiram Clawson, James Cuff, Federica Di Palma, Stephen Fitzgerald, Paul Flicek, Mitchell Guttman, Melissa J. Hubisz, David B. Jaffe, Irwin Jungreis, W. James Kent, Dennis Kostka, Marcia Lara, Andre L. Martins, Tim Massingham, Ida Moltke, Brian J. Raney, Matthew D. Rasmussen, Jim Robinson, Alexander Stark, Albert J. Vilella, Jiayu Wen, Xiaohui Xie, Michael C. Zody, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Kim C. Worley, Christie L. Kovar, Donna M. Muzny, Richard A. Gibbs, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Wesley C. Warren, Elaine R. Mardis, George M. Weinstock, Richard K. Wilson, Genome Institute at Washington University, Ewan Birney, Elliott H. Margulies, Javier Herrero, Eric D. Green, David Haussler, Adam Siepel, Nick Goldman, Katherine S. Pollard, Jakob S. Pedersen, Eric S. Lander & Manolis Kellis.
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011).