The genome browsers include several annotations of the reference genome, which include the more basic and general information, like the genes or the GC content, but also more specific tracks relevant for nucleosome studies, like information about chromatin structure from histone modification studies, transcription factors, nucleosome organization, etc.
Tracks by reference genome:
| Data | Source |
|---|---|
| Saccharomyces cerevisiae • Genome Browser | |
| Gene and Gene predictions | Saccharomyces Genome Database |
| Gene structure / UTRs / transcribed regions | Yassour et al, 2009 |
| Gene Models / introns / 5’ 3’ UTR’s / unannotated transcripts | Nagalakshimi et al. 2008 |
| Transciption Start sites | Zhang, Z and Dietrich FS. 2005 |
| Chromatin modifications | Kirmizis A. et al. 2007 |
| Nucleosome positions | Mavrich et al. 2008 |
| Digital genomic footprinting | Hesselberth et al. 2009 |
| H2A.Z nucleosome positions | Albert et al. 2007 |
| H2A/H2B, H2A.Z/H2A.Z, H2A.Z/H2B log2 ChIp chip ratio | Guillemette et al. 2005 |
| H3K4ac_set1D_on_WT, set1D_H3K4ac_on_H3, WT_H3K4ac_on_H3, WT_H3K4me3_on_H3 | Guillemette et al. 2011 |
| anti-Ac, H2AK7aci, H2BK16ac, H3K14ac, H3K18ac, H3K4me1, H3K4me2, H3K4me3, H3K9ac, H4K12ac, H4K16ac, H4K5ac, H4K8ac, mock, RNA PolII ChIP_chip | Liu et al. 2005 |
| predicted average nucleosome occupancy, predicted nucleosome potential score, nucleosome sequence read count | Field et al. 2008 |
| nucleosome positions, nucleoatac signal, nucleosome calling occurrences | Schep et al. 2015 |
| ORC, Mcm2p binding, ARS sequences | Xu et al. 2006 |
| ORC, ARS, Nucleosome positioning | Eaton et al. 2010 |
| TATA_elements | Rhee and Ough 2012 |
| Bur1, Cet1 (Capping enzyme), Ctk1 Elf1, Kin28 (TFIIH), Paf1, Pcf11, Ser2P (RNA Pol II), Ser5P (RNA Pol II), Ser7P (RNA Pol II), Rpb3 (RNA Pol II), Spn1 (lws1), Spt16, Spt4, Spt5, Spt6, Spt6deltaC, Tfg1 (TFIIF), TFIIB |
Mayer et al. 2010 |
| Gal4, Phd1, Rap1, Reb1 | Rhee and Pugh 2011 |
| Nucleosome architecture through cell cycle | Deniz et al. 2016 |
| Drosophila melanogaster • Genome Browser | |
| Genes, Transcripts | Flybase database |
| Chromatin types through protein binding sites | Filion et al. 2010 |
| Nucleosome organization | Mavrich et al 2008 |
| Chromatin insulators, Histone marks (antibody2, H1, H2, H2Av, H3, H3K18, H3K23, H3K27, H3K36, H3K4, H3K79, H3K9, H4), Heterochromatin proteins, Histone modifiers, Nucleosome remodelers, Polycomb, Polymerase, GAF, dSFMBT, POF, POF, dSFMBT, POF, Chro(Chriz)WR, MBD-R2(Q4167) | modENCODE Project |
| Homo sapiens • Genome Browser | |
| Refseq Genes | RefSeq Database |
| Gencode Genes | GENCODE Project |