Integrated Regulation from ENCODE: This collection of tracks displays integrated signal and clustering annotations from multiple cell lines, using ENCODE primary data from RNA-seq, ChIP-seq, and DNase-seq assays. This track is a companion to the hg18 ENCODE Regulation track.
Open Chromatin by DNaseI HS from ENCODE/OpenChrom(Duke University): This track displays DNaseI hypersensitivity evidence as part of the four Open Chromatin track set.
RNA Binding Protein Associated RNA by RIP-chip GeneST from ENCODE/SUNY Albany: This track displays transcriptional fragments associated with RNA binding proteins in different cell lines using RIP-Chip (Ribonomic) -profiling on Affymetrix GeneChip® Human Gene 1.0 ST Arrays. +profiling on Affymetrix GeneChip� Human Gene 1.0 ST Arrays.
DNaseI Hypersensitivity by Digital DNaseI form ENCODE/University of Washington: This track shows DNaseI sensitivity measured genome-wide in different cell lines using the Digital DNaseI methodology.
OrChID Predicted DNA Cleavage Sites from ENCODE/Boston Univ (Tullius Lab): This track display predicted hydroxyl radical cleavage intensity on naked DNA for each nucleotide in the genome.
Histone Modifications by ChIP-seq from ENCODE/Stanford/Yale/Davis/Harvard: This track displays maps of histone modifications genome-wide using ChIP-seq in different cell lines.
Several new ENCODE data sets have been released in the UCSC Genome Browser.
EGASP Full, Partial, and Update: These three gene prediction tracks are from the ENCODE Gene Annotation Assessment Project (EGASP) Prediction Workshop 2005. The EGASP Full track shows 20 sets of gene predictions originally submitted for the workshop, covering all 44 ENCODE regions. THE EGASP Partial track shows eight sets of gene precdictions that were submitted for the workshop, but do not cover all ENCODE regions. The EGASP Update track shows updated versions of some of the submitted predictions. Thanks to Julien Lagarde at IMIM for providing the EGASP Full and EGASP Partial data sets. Thanks to Tyler Alioto of IMIM (GeneID-U12 and SGP2-U12), Deyou Zheng of Yale (Yale - Pseudogenes), Sarah Djebali of Ecole Normale Supérieure + Pseudogenes), Sarah Djebali of Ecole Normale Sup�rieure (Exogean), Jonathan Allen of TIGR/Univ. Maryland (Jigsaw) and Mario Stanke of the University of Gottingen (Augustus) for providing their EGASP Update gene sets.
RIKEN CAGE Predicted Gene Start Sites: This track shows the numbers of 5' cap analysis gene expression (CAGE) tags that map to the genome at specific locations. Areas in which many tags map to the same region may indicate a significant transcription start site. Thanks to Albin Sandelin at RIKEN and the FANTOM (Functional Annotation of Mouse) Consortium for providing these data.
Stanford RTPCR: This track displays absolute transcript copy numbers for 136 genes and 12 negative control intergenic regions, determined by real-time PCR in