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Supplemental Figure & Table Guide
Figure S1: Chromosome 11 recombination rate versus sequence-based physical distance.
Markers from the deCODE genetic map were aligned to the chromosome and the average
recombination rate was calculated for each 1 Mb window along its length. Female, male, and
sex-averaged recombination rates are indicated in pink, blue and yellow, respectively. [Adobe
PDF, 528 KB]
Figure S2: Gene and disorder distributions across the human genome. Chromosome 11 is
extremely gene and disorder rich compared to other human chromosomes. The number and
density of genes and disorders which had been mapped in the Ensembl browser
(http://www.ensembl.org/index.html) as of April 2005 were plotted relative to their
corresponding chromosome size. [Adobe PDF, 510 KB]
Figure S3: Sequence similarity and aligned bases of segmental duplications. For all pairwise
alignments, the total number of aligned bases was calculated and binned based on percent
sequence identity. Sequence identity distributions for interchromosomally (red) and
intrachromosomally (blue) duplicated bases are shown. [Adobe PDF, 511 KB]
Figure S4: Divergence of chromosome 11 segmental duplications. The scatter plot depicts the
length (log 10) and divergence of inter- (red) and intra- (blue) chromosomal segmental
duplication. Divergence (K) is calculated as the number of substitutions per site between the
two sequences. [Adobe PDF, 589 KB]
Figure S5: Pattern of chromosome 11 segmental duplications. The parasight view depicts the
pattern of interchromosomal (red) and intrachromosomal (blue) duplications (>5 kb, >95%)
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for chromosome 11. Chromosome 11 is drawn at 20X greater scale of the other chromosomes.
Centromeres are shown as purple bars. [Adobe PDF, 512 KB]
Figure S6: Distribution of segmental duplications. A schematic of chromosome 11 segmental
duplications depicting the location of interchromosomal (red) and intrachromosomal (blue)
duplicated sequence. Each horizontal line represents 15 Mb of sequence, with tick marks
every 1 Mb. Sequencing gaps are represented as discontinuities within the horizontal line.
The centromere is shown as a purple bar. Duplications detected by whole genome shotgun
sequence are represented as black bars above the chromosome sequence38. [Adobe PDF, 527
KB]
Figure S7: Sequence identity of segmental duplications on chromosome 11.
Interchromosomal (red) and intrachromosomal duplications (blue) are shown to scale along
the horizontal line in 1Mb increments. Black bars above the horizontal line correspond to
duplications as detected by the whole-genome shotgun sequence detection method. The
underlying pairwise alignments of segmental duplications (>90% >1kb) are depicted as a
function of % identity below the horizontal line. Different colors correspond to the location
of the pairwise alignment on different human chromosomes. (i.e. chromosome 11 is shown as
magenta, chromosome 18 as light blue). [Adobe PDF, 557 KB]
Figure S8: Multi-species comparative genome analysis for chromosome 11. a) The map of
conserved synteny between human chromosome 11 and chimpanzee, mouse, rat, dog and
chicken genomes. Syntenic chromosome blocks are distinguished by color. Orientation is
indicated by arrows within each block. b) Gene density was calculated as number of
expressed genes per 500 Kb. c) The density of conserved non-coding elements (CNEs) per
500 Kb when the chromosome was aligned to both mammals (mouse, rat and dog) and
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mammals plus chicken. The centromere and clone gaps are indicated by vertical gray boxes.
[Adobe PDF, 550 KB]
Figure S9: Distribution of conserved non-coding regions along human chromosome 11. a)
CNE distribution for human versus mammals (chimpanzee, dog, mouse, rat) and b) human
versus mammals plus chicken. [Adobe PDF, 616 KB]
Figure S10: Segmentally duplicated region that was challenging to finish. Dot plot of 566 Kb
region on HSA11q containing large, inverted segmental duplication. Sequence identity is
indicated by color scale at bottom right of figure. [Adobe PDF, 798 KB]
Table S1: Minimum clone tiling path of human chromosome 11. [Excel 2003, 282 KB]
Table S2: Physical/clone libraries screened during map construction. [Excel 2003, 18 KB]
Table S3: Finished contigs and gaps on human chromosome 11. [Excel 2003, 17 KB]
Table S4: Sequence quality information for RIKEN and WUGSC chromosome 11 clones.
[Excel 2003, 22 KB]
Table S5: Interspersed repetitive elements. Repeats were identified with both the
RepeatMasker and Tandem Repeats Finder programs. There is a substantial overlap in the
results between the two programs. In some cases the total length occupied for a class is lower
than the sum of the individual family members due to overlapping elements. [Word 2003, 62
KB]
Table S6: Gene catalog of human chromosome 11. [Excel 2003, 987 KB]
Table S7: Non-OR clustered gene families on human chromosome 11. [Excel 2003, 32 KB]
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Table S8: Read-through transcripts found on human chromosome 11. [Excel 2003, 25 KB]
Table S9: CpG islands versus number of variants in expressed genes. [Excel 2003, 17 KB]
Table S10: Olfactory receptor gene clusters on chromosome 11. [Word 2003, 104 KB]
Table S11: Predicted CpG islands on human chromosome 11. [Excel 2003, 170 KB]
Table S12: Gene expression analysis results for DIGIT predicted genes. [Excel 2003, 20 KB]
Table S13: Accession numbers for submitted DIGIT mRNA sequences. [Excel 2003, 26 KB]
Table S14: Blast results for DIGIT genes versus the NCBI nt database. [Excel 2003, 79 KB]
Table S15: InterProScan analysis of DIGIT verified genes. [Excel 2003, 50 KB]
Table S16: OMIM disorders that have been associated with human chromosome 11 but for
which no specific cause has yet been determined. The table was compiled from data available
in OMIM (http://www.ncbi.nlm.nih.gov/Omim) in June 2005. [Excel 2003, 119 KB]
Table S17: Gene deserts on human chromosome 11. [Excel 2003, 20 KB]
Table S18: Imprinted genes on human chromosome 11. [Word 2003, 49 KB]
Table S19: Bases involved in segmental duplication and pairwise alignment. [Excel 2003, 15
KB]
Table S20: Segmental duplication positions on human chromosome 11. [Excel 2003, 91 KB]
Table S21: Segmental duplication in pericentromeric and telomeric regions. Segmental
duplication within 5 Mb around centromere and the telomere of chromosome 11 are
considered as pericentromeric and subtelomeric respectively. [Excel 2003, 15 KB]
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Table S22: RefSeq genes overlapped with segmental duplication. RefSeq genes with at least
one exon fully duplicated are listed. Exons with at least 50 bp of duplication were deemed
duplicated. A gene could be duplicated multiple times at different percent identity. [Excel
2003, 30 KB]
Table S23: Conservation blocks and segments between chromosome 11 and other genomes.
[Excel 2003, 17 KB]
Table S24: Conserved non-coding elements on human chromosome 11. [Excel 2003, 479
KB]
Table S25: Sequencing gaps on human chromosome 11. [Excel 2003, 20 KB]
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