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Comparative analysis

Vega contains comparative pairwise analysis between specific genomic regions from either different species or from different haplotypes / strains. This is in contrast to Ensembl where many all genome versus all genome comparisons are performed. The analysis in Vega involves:

  • The identification of genomic alignments using LastZ.
  • Prediction of the orthologue pairs using the Ensembl gene tree pipeline. Note that although the pipeline generates phylogenetic genetrees, the limited scope of the Vega comparative analysis means that these will neccesarily be incomplete and consequently only orthologs are shown on the website. Human LoF genes are excluded from these predictions.
  • The manual identification of alleles in either different human haplotypes or mouse strains.
The results of the analysis can be viewed in different ways:
  • Whole genome alignments can be displayed on 'Region in detail' by checking the box(es) in the 'LASTZ alignments' configuration menu.
  • The annotations can be compared in more detail using three other Location based views:
    • 'Alignments (image)' shows a graphical representation of the actual pairwise alignment.
    • 'Alignments (text)' shows the alignment of the sequences.
    • 'Region comparison' shows multiple slice in the region of the alignment. Joining of orthologue predictions and haplotype alleles can enabled by checking the 'Join genes' box in the Comparative Features configuration panel.
  • Details of the ortholog predictions and allele annotations are shown on the 'Orthologs' and 'Alleles' panels of gene pages.

There are six sets of analyses:

  1. The MHC region has been compared between tasmanian devil, dog, pig (two assemblies), rat, gorilla, chimpanzee, wallaby, mouse and eight human haplotypes:
    • tasmanian devil chromosome 4-MHC
    • dof chromosome 12-MHC
    • gorilla chromosome 6-MHC
    • chimpanzee chromosome 6-MHC
    • wallaby chromosome 2-MHC
    • pig chromosome 7 on Sscrofa10.2 (24.7Mb to 29.8Mbp)
    • pig chromosome 7-LW
    • rat chromosome 20 (1.33Mbp to 5.67Mbp)
    • mouse chromosome 17 (clones CT033847.5 to AC134471.3; 33.4Mbp to 38.9Mbp)
    • mouse chromosome 17 MHC region in the NOD/MrkTac and NOD/ShiLtJ strains
    • chromosome 6 on the human reference assembly (28Mbp to 34Mbp)
    • chromosome 6 MHC region in the human COX, QBL, APD, DBB, MANN, MCF and SSTO haplotypes (full length chromosome fragments)
  2. Comparisons between the LRC regions of pig, gorilla and human (nine haplotypes):
    • pig chromosome 6 (53.6Mbp to 54.0Mbp)
    • gorilla chromosome 19-LRC
    • human chromosome 19q13.4 (54.6Mbp to 55.6Mbp) on the reference assembly.
    • chromosome 19 LRC region in the COX_1, COX_2, PGF_1, PGF_2, DM1A, DM1B, MC1A and MC1B haplotypes (full length chromosome fragments).
  3. Insulin dependent diabetes (Idd) regions on six mouse chromosomes (1, 3, 4, 6, 11 and 17) have been compared between the CL57BL/6J reference and one or more of the NOD/MrkTac (17-Idd1_DIL), NOD/ShiLtJ (17-Idd1_CHO), and the 129 strains. Further details are described here.

    The regions of the CL57BL/6J reference assembly used in these comparisons are:

    • Idd1: chromosome 1, clones CT033847.5 to AC134471.3
    • Idd3: chromosome 3, clones AC117584.11 to AL627074.11
    • Idd4.1: chromosome 11, clones AL596185.12 to AL663042.5
    • Idd4.2: chromosome 11, clones AL663082.5 to AL604065.7
    • Idd4.2Q: chromosome 11, clones AL596111.7 to AL645695.18
    • Idd5.1: chromosome 1, clones AL683804.15 to AL645534.20
    • Idd5.3: chromosome 1, clones AC100180.12 to AC101699.9
    • Idd5.4: chromosome 1, clones AC123760.9 to AC109283.8
    • Idd6.1 + Idd6.2: chromosome 6, clones AC164704.4 to AC164090.3
    • Idd6.AM: chromosome 6, clones AC171002.2 to AC163356.2
    • Idd9.1: chromosome 4, clones AL627093.17 to AL670959.8
    • Idd9.1M: chromosome 4, clones AL611963.24 to AL669936.12
    • Idd9.2: chromosome 4, clones CR788296.8 to AL626808.28
    • Idd9.3: chromosome 4, clones AL607078.26 to AL606967.14
    • Idd10: chromosome 3, clones AC167172.3 to AC131184.4
    • Idd16.1: chromosome 17, clones AC125141.4 to AC167363.3
    • Idd18.1: chromosome 3, clones AL845310.4 to AL683824.8
    • Idd18.2: chromosome 3, clones AC123057.4 to AC129293.9
  4. Comparisons between three specific regions:

    • pig chromosome 17 (58.2Mbp to 67.4Mbp)
    • human chromosome 20q13.13-q13.33 (45.8Mbp to 62.4Mbp)
    • mouse chromosome 2 (168.3Mbp to 179.0Mbp)
  5. Pairwise comparisons between two pairs of full length mouse and human chromosomes:

    • human chromosome 1 and mouse chromosome 4
    • human chromosome 17 and mouse chromosome 11
    • human chromosome X and mouse chromosome X
  6. Pairwise comparisons between chromosome X from human, mouse and pig.