Statistics of the Database

May, 2003 (updated for DBTSS ver.3)

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Contents of Statistics Statistics of the Database

Table 1. Statistics of the Database Table 2. Statistics of Full-length cDNA Sequences Used for the Database Construction Figure 1. Comparison between Ref-fulls and RefSeqs Figure 2. Distribution of the Numbers of Mapped Full-length cDNAs Figure 3. Distribution of the Sequence Conservation between Human and Mouse Promoter Pairs Figure 4. Schematic representation of the data flow Library List: H.sapiens Library List: M.musclus

Statistics of the Database Statistics of the Database

Table 1. Statistics of the Database Human Mouse RefSeq and Ref-full    Ref-full (promoter retrieval successful) 8,793 (48%) 6,875 (53%)    Ref-full (total) 9,270 (51%) 7,524 (58%)    Ref-full that extended RefSeq 6,042 (33%) 5,018 (38%)    Ref-full that did not extend RefSeq 3,228 (18%) 2,506 (19%)    RefSeq that are not covered by Ref-full 8,944 (49%) 5,557 (42%)    RefSeq (total) 18,214(100%) 13,081 (100%)   One-pass sequences and genome mapping         Hit to RefSeq (genome mapping successful) 190,964 (48%) 195,446 (34%)    Hit to RefSeq (genome mapping ambiguous) 36,267 (9%) 36,624 (6%)    No hit to RefSeq 172,994 (43%) 348,139 (60%)    One-pass (total) 400,225 (100%) 580,209 (100%)   Statistics of the number of promoters, the redundancies of the supporting full-length cDNAs and the differences between the public data are shown.

Statistics of Full-length cDNA Sequences Used for the Database Construction Statistics of the Database

Table 2. Statistics of Full-length cDNA Sequences Used for the Database Construction number of registered genes (average redundancy) average length difference against RefSeq (mRNA level) average length difference against RefSeq (genomic level)    Human 8,793 (21.7) 71.6 4,396    Mouse 6,875 (28.4) 76.0 4,027    human/mouse pair 3,324 (25.2/38.0) 63.3/68.8 3,998/3,380   Statistics of the full-length cDNAs used for the database construction is shown.

Comparison between Ref-fulls and RefSeqs Statistics of the Database

Figure 1. Comparison between Ref-fulls and RefSeqs The distributions of the differences between Ref-fulls and RefSeqs are presented, when compared at the mRNA level (A) and genomic level (B). Black and gray bars represent the cases for human and mouse genes, respectively.

Distribution of the Numbers of Mapped Full-length cDNAs Statistics of the Database

Figure 2. Distribution of the Numbers of Mapped Full-length cDNAs The distribution of the numbers of mapped TSSs is shown for human and mouse genes by black and gray bars, respectively.

Distribution of the Sequence Conservation between Human and Mouse Promoter Pairs Statistics of the Database

Figure 3. Distribution of the Sequence Conservation between Human and Mouse Promoter Pairs Sequence alignments were performed using LALIGN using the default parameters. The sequence identity was evaluated as the number of aligned nucleotides in the regions of -1000 to +200 (TSS: 0).

Schematic representation of the data flow Statistics of the Database

Figure 4. Schematic representation of the data flow The boxes that are marked with asterisks (A~G*) correspond to the respective forms illustrated in Figure 5.

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