Table 4 |
||
|
Experimental feature definitions |
||
| Feature |
Term |
Definition |
|
|
||
| RNA transcription (coding and noncoding) |
CDS |
Coding sequence: well characterized transcribed regions with an annotated protein-coding
open reading frame (ORF) |
| RACEfrags |
5' and 3' rapid Amplification of cDNA ends (RACE), using polyA or total RNA to construct
full-length cDNA. This technique has revealed previously unrecognized UTRs |
|
| TARs/transfrags |
Transcriptionally active regions/transcribed fragments as determined by analyses of
cellular RNA (polyA or total) hybridizations to multiple microarray platforms. For
the analyses reported here, portions of TARs/transfrags overlapping any CDS, 5' or
3' UTR annotations were removed from the dataset |
|
| Pseudo-exons |
A pre-mRNA sequence that resembles an exon but is not recognized as such by the splicing
machinery |
|
| TSS |
Transcription start site |
|
| 5' UTR |
Untranslated region: portions of CDS-containing transcripts before the start codon.
For the analyses reported here, 5' UTRs overlapping alternatively transcribed CDS
annotations were removed from the dataset |
|
| TUF |
Transcripts of unknown function for noncoding transcripts |
|
| 3' UTR |
Untranslated region: portions of CDS-containing transcripts after the stop codon |
|
| Transcript regulation: open chromatin/DNA-protein interaction |
DHS |
DNAse I hypersensitive sites are short regions of DNA that are relatively easily cleaved
by deoxyribonuclease. Regions of open chromatin detected by quantitative chromatin
profiling and novel microarray-based methods. For the analyses reported here, regions
that overlap repetitive sequence were removed. Measures of DHS are reported using
two sources: the ENCODE Regulome group and the NHGRI |
| FAIRE-sites |
Formaldehyde assisted isolation of regulatory elements: a procedure used to isolate
chromatin that is resistant to the formation of protein-DNA crosslinks. Data suggest
that depletion of nucleosomes (the most basic organizational unit of chromatin) at
active regulatory regions, such as promotors, is the primary underlying basis for
FAIRE [38] |
|
| HisPolTAF |
Histone modifications, RNA polymerase II (PolII), and transcription regulator TAF250 |
|
| Sequence specific factors |
Regions of DNA determined to be bound by sequence-specific transcription factors through
chromatin immunoprecipitation followed by microarray chip hybridization (so-called
'ChIP-Chip') analyses |
|
| Sequence specific (all motifs) |
Computationally identified short sequence motifs found to be over-represented in the
sequence specific factors dataset |
|
| Ancestral repeats |
Mobile elements with well defined consensus sequences that inserted into the ancestral
genome prior to mammalian radiation. These sequences are considered to be predominantly
non-functional and are often used as models of neutrally evolving DNA |
|
| Cell cycle |
EarlyRepSeg |
Early replicating segments |
| MidRepSeg |
Mid replicating segments |
|
| LateRepSeg |
Late replicating segments |
|
| Evolutionary constraint |
MCS strict |
Multi-species conserved sequences: strict criteria |
| MCS moderate |
Multi-species conserved sequences: modest criteria |
|
| MCS loose |
Multi-species conserved sequences: loose criteria |
|
|
|
||
|
Clark et al. Genome Biology 2007 8:R180 doi:10.1186/gb-2007-8-9-r180 |
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