Human Genome HG18 Annotation Files
A complete suite of annotation files is provided with NimbleGen Human (hg18 build) CGH/CNV Arrays. For more information about these files consult the table below.
Download the complete 9-file set!
Note: You can import and view these files alongside your microarray data using SignalMap software. Features in some of these files may be more easily viewed by changing the feature style from dots to bars in SignalMap. To do this, select the track by clicking its Y axis and select Track -> Style -> Bars.
| File Name | Description |
| Genes.gff | Indicates all genes for build hg18 as reported in the UCSC Genome browser (http://genome.ucsc.edu). Genes annotated above the baseline in each track represent features identified on the sense strand, while entries below the baseline represent features identified on the antisense strand. |
| Genes_Exon-Intron.gff | Indicates the exon-intron boundaries of all genes in build hg18 as reported in the UCSC Genome browser. Exons are denoted as dark blue bars, and introns are denoted as light blue bars. |
| Transcription_Start_Sites.gff | Indicates all transcription initiation sites for build hg18 as reported in the UCSC Genome browser. |
| Structural_Variants.gff | Displays all copy number variants as reported in the Database of Genomic Variants (http://projects.tcag.ca/variation). |
| 42M_CNV_Regions.gff* | Displays validated CNVs identified by the Genome Structural Variation Consortium in a high-resolution CNV discovery project (http://www.sanger.ac.uk/humgen/cnv/42mio). In this study, common CNVs > 500 bp were identified from 20 CEU and 20 YRI HapMap research samples using a set of NimbleGen CGH arrays that contains approximately 42 million probes tiled across the genome. |
| NimbleGen_CNV_Regions.gff* | Displays CNVs from Asian research samples identified by Roche NimbleGen using high-resolution NimbleGen CGH arrays. |
| Segmental_Duplications.gff | Displays regions of genomic duplication > 1 kb in size and with > 90% sequence identity after masking high-copy repeat regions (Bailey, et al. 2001; 11:1005-17) and reported in the UCSC Genome browser. The level of similarity is indicated as follows: light to dark gray bars = 90 - 98% similarity, light to dark yellow bars = 98 - 99% similarity, light to dark orange bars ≥ 99% similarity; red = duplications of > 98% that lack sufficient evidence in the Segmental Duplication database. |
| Cytogenetic_Ideogram.gff | Displays the cytogenetic bands, in grayscale format, for each chromosome as reported in the UCSC Genome browser. |
| miRNA.gff | Indicates all miRNAs as reported in the miRBase database (http://microrna.sanger.ac.uk/). Each feature represents the entire hairpin sequence for the miRNA. |
| * All of the CNVs shown in this file are included on NimbleGen Human (hg18 build) CNV Arrays. | |
Download the complete 9-file set!
