Attribute List for Genome Assembly: panTro2


This page summarizes the different attribute groups included in EpiGRAPH and provides references to the source from which the datasets were obtained. Further information can be obtained from the EpiGRAPH Background page and from the EpiGRAPH attribute reference sheet.



DNA_Sequence


Attributes that describe the DNA sequence itself, including base composition and oligonucleotide patterns


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Base_compositionStrand-specific frequency of occurence for each nucleotide (A, C, G and T)Calculated directly from the DNA sequence
All_2mersFrequency of occurence separately for each oligonucleotides of size two that does not include any Ns (not strand-specific)Calculated directly from the DNA sequence
All_4mersFrequency of occurence separately for each oligonucleotides of size four that does not include any Ns (not strand-specific)Calculated directly from the DNA sequence


DNA_Structure


Attributes that describe the DNA structure (as inferred from the DNA sequence), such as distortions of the DNA helix and predicted solvent accessibility


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Predicted_Helix_StructureHelix structure of naked DNA as predicted from octamers with known structureCalculated by a simple sliding window approach using the simulation data reported in Gardiner et al. (2003) J Mol Bioltwist
roll
tilt
rise
slide
shift
Predicted_Solvent_Accessible_SurfaceSolvent accessible surface area of naked DNA as predicted from trimers with known valuesCalculated similarly to the UCSC Genome Browser Boston University ORChID track (http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=78806550&c=chr7&g=encodeBu_ORChID1)pk1_mean
pk2_mean
pk3_mean


Repetitive_DNA


Attributes that describe repetition within the DNA, including transposable elements, tandem repeats and segmental duplications


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
RepeatMaskerRepeats as detected by RepeatMasker. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro2&c=chr7&g=rmsk for details.UCSC Genome Browser, tables chr1_rmsk to chrY_rmskswScore
repStart
repLeft
repClass
repFamily
Simple_RepeatsTandem repeats as detected by Tandem Repeats Finder. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro2&c=chr7&g=simpleRepeat for details.UCSC Genome Browser, table simpleRepeatperiod
copyNum
score
entropy


Chromosome_Organisation


Attributes that describe the large-scale functional organisation of the chromosomes, including isochores and special-interest regions


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns


Evolutionary_History


Attributes that describe the evolutionary history of the genome, including conservation and local recombination rates


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns


Population_Variation


Attributes that describe the variability among today's individuals, including SNPs and microdeletions


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns


Genes


Attributes that describe the distribution of known and predicted protein-coding genes, pseudogenes and non-coding genes within the genome


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
RefSeq_GenesKnown protein-coding genes taken from the NCBI mRNA reference sequences collection (RefSeq). See http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro2&c=chr2&g=refGene for details.UCSC Genome Browser, table refGene


Regulatory_Regions


Attributes that describe predicted regulatory regions and elements of the genome


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
CpG_IslandsCpG islands according to a UCSC Genome Browser detection algorithm. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro2&c=chr7&g=cpgIslandExt for details.UCSC Genome Browser, table cpgIslandExtperGc
obsExp


Transcriptome


Attributes that describe the transcriptional activity, including non-genic transcription and promoter activity


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns
Species_mRNAsAnnotation of alignments between species-specific mRNAs in GenBank and the genome. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro2&c=chr2&g=mrna for detailsUCSC Genome Browser, table all_mrna
Spliced_ESTsAnnotation of alignments between species-specific spliced ESTs in GenBank and the genome. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro2&c=chr2&g=intronEst for detailsUCSC Genome Browser, tables chr*_intronEst
Species_ESTsAnnotation of alignments between species-specific ESTs in GenBank and the genome. See http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=panTro2&c=chr2&g=est for detailsUCSC Genome Browser, table all_est


Epigenome_and_Chromatin_Structure


Attributes that describe the chromatin structure and epigenetic modifications, including histone modifications and protein binding


Attribute nameDescriptionData source for attributeScore columnsClass columnsCategory columns