Extensive Gene Traffic on the Mammalian X Chromosome J. J. Emerson, Henrik Kaessmann, Esther Betrán, and Manyuan Long

This supplement contains:

1. Materials and Methods
2. Fig. S1
3. Tables S1 to S9
4. References

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Tables S1 to S9. Excel data tables (compressed archive of one Excel file containing nine tables, in *.zip format; users should download the compressed file to their machine and decompress the file on their local hard drive, using the instructions below).
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Table S1. Annotation of the genes used in this analysis and their support criteria for humans. Alignment length between retrogene and parental gene is given in nucleotides. "% id" indicates amino acid identity of the alignment. Functionality criteria are described in Methods. "EST" indicates that the retrogene matched ESTs belonging to Unigene clusters that contain ESTs from different genes. Therefore, tissue expression could not be unambiguously determined (n.d.). "Male expression" indicates retrogene expression in testis; "Female expression" indicates retrogene expression in ovary, breast, cervix, and/or uterus tissues. This table contains gene pairs for which the parental gene gave rise to multiple retrogenes. These redundant pairs were removed for all statistical analyses.

Table S2. Annotation of the genes used in this analysis and their support criteria for mouse. Alignment length between retrogene and parental gene is given in nucleotides. "% id" indicates amino acid identity of the alignment. Functionality criteria are described in Methods. This table contains gene pairs for which the parental gene gave rise to multiple retrogenes. These redundant pairs were removed for all statistical analyses.

Tables S3 and S4. Results for outlier tests in humans (Table S3) and mouse (Table S4). Tests were conducted on the ratio of observed / expected. In all cases but for gene export in human pseudogenes, the Grubbs (P < 0.01) and Dixon (P < 0.005) tests indicate that X is an outlier (S8). For pseudogene export, the X is not an outlier. Additionally, for every case, tests of normality indicate using the Shapiro-Wilks test (S9), that when X is removed as an outlier, none of the distributions violate the hypothesis of neutrality (P > 0.1).

Table S5. Mammalian functional genes generated by retroposition in a literature search. They are reported if the location of parental and derived was known. ?Ubiquitous? implies that the gene is expressed in many tissues. Cases that are consistent with the out of X pattern are shown in bold. Ensembl identifiers for retrogenes are indicated for X-linked genes revealed by our screen.

Table S6. Genes specifically expressed during mammalian male meiosis. Gene information comes from Eddy & O'Brien (S10). Location comes from the NCBI database: www.ncbi.nlm.nih.gov/Locuslink. The only gene that maps on the X chromosome is known to play a role in X inactivation (S11).

Table S7. Dating of the retroposition events in and out of the X-chromosome for humans. KS between parental and mouse orthologs and synteny information is given. Age is decided based on this information (see Methods).

Table S8. Dating of the retroposition events in and out of the X-chromosome for mouse. KS between parental and mouse orthologs and synteny information is given. Age is decided based on this information (see Methods).

Table S9. Contingency tables (2 2) used in the Fisher?s exact tests for the comparison of the ratio of X-linked to autosomal genes in functional versus pseudogenes for both export and import.

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