| DART | Transcriptionally Active Regions (TARs) for ENCODE |
This is the database of Transcriptionally Active Regions (TARs), otherwise known as transcribed fragments (transfrags), generated by the ENCODE Genes and Transcripts Group. The transcripts were detected by two sets of experiments using the Affymetrix ENCODE tiling array in the laboratories of Michael Snyder (Yale), Sherman Weissman (Yale), Mark Gerstein (Yale) and Tom Gingeras (Affymetrix). The sets of TARs (transfrags) stored here are for 11 different samples which encompass different RNA types. |
Selected Union Sets
| Set name | Set description | Size |
| union of Yale TARs | Union of TARs from the Yale datasets (NB4_CTRL, NB4_RA, NB4_TPA, Neutrophil, Placenta) with TARs(transfrags) removed that overlap either pseudogenes or low complexity repeats within the ENCODE regions | 4334 |
| union of Affy TARs | Union of transfrags from the Affymetrix datasets (HeLa, GM06990, HL60_00, HL60_02, HL60_08, HL60_32) with TARs(transfrags) removed that overlap either pseudogenes or low complexity repeats within the ENCODE regions | 9056 |
| union of polyA RNA TARs | Union of TARs/transfrags from Poly(A)+ RNA samples (HeLa, GM06990, HL60_00, HL60_02, HL60_08, HL60_32, Placenta) with TARs(transfrags) removed that overlap either pseudogenes or low complexity repeats within the ENCODE regions | 9277 |
| union of total RNA TARs | Union of TARs/transfrags from Total RNA samples ( NB4_CTRL, NB4_RA, NB4_TPA) with TARs(transfrags) removed that overlap either pseudogenes or low complexity repeats within the ENCODE regions | 2709 |
| union of all Tars | Union of All RNA Samples (HeLa, GM06990, HL60_00, HL60_02, HL60_08, HL60_32, NB4_CTRL, NB4_RA, NB4_TPA) with TARs(transfrags) removed that overlap either pseudogenes or low complexity repeats within the ENCODE regions | 9852 |
| novel TARs | novel TARs | 6988 |
|
novel TARs associated with known genes |
novel TARs associated with known genes | 955 |
|
novel TARs In novel loci clusters from expression profiles |
novel TARs In novel loci clusters from expression profiles | 681 |
|
novel TARs in novel loci clusters from phylogenetic profiles |
novel TARs in novel loci clusters from phylogenetic profiles | 782 |
|
novel TARs with peculiar sequence composition |
novel TARs with peculiar sequence composition | 503 |
|
novel TARs with tandem matches |
novel TARs with tandem matches | 249 |
| Database for Active Regions with Tools (DART) | |||
| Yale Bioinformatics Report problems | |||