Statistics of the Database

---

Contents of Statistics Statistics of the Database

Table 1. Statistics of the Database Table 2A. Statistics of the cDNA Table 2B. Statistics of the Solexa datasets Figure 1. Identification of the Putative Alternative Promoters (PAPs) in Human Genes Table 3. Statistics of the Putative Alternative Promoters (PAPs) Figure 2. Schematic representation of the data flow Figure 3. classification of the TSSs using different cut-offs and criteria Figure 4. Size of the one TSS cluster Library List: H.sapiens Library List: M.musclus

Statistics of the Database Statistics of the Database

Table 1. Statistics of the Database #covered locus #promoter #total TSSs #allocated clones human 15,262 30,964 425,117 1,359,000 mouse 14,162 19,023 149,876 364,487 zebrafish 3,061 3,382 15,198 32,263 malaria 1,527 N.A. 6,908 10,236 schyzon 3,635 N.A. 14,029 22,923

Statistics of the cDNA Statistics of the Database

Table 2A. Statistics of the cDNA human mouse zebrafish malaria schyzon Total cDNAs 1,780,295 580,209 159,981 12,484 30,766 Mapped cDNAs 1,548,357 457,007 98,164 9,498 27,947 Possible truncated cDNAs 181,237 28,081 12,198 2,691 76 RefSeq hit cDNAs 1,359,000 364,487 32,263 10,236 22,923 *Covered RefSeq 14,628 13,704 3,061 1,218 3,627 Promoters 30,964 19,023 3,382 1,734 4,067 *RefSeq total 17,217 (Human), 16,138 (Mouse), 4,234 (Zebrafish), 5,409 (Malaria), 4,539 (schyzon)

Statistics of the Solexa datasets Statistics of the Database

Table 2B. Statistics of the Solexa datasets Statistics of the datasets produced by the Solexa sequencer (upper two rows) and by the original Sanger sequencer (bottom row) in humans. TSSs which were supported by equal or greater than 5 sequences were counted for the Solexa datasets. total #mapped sequences #sequences associated with NMs #represented NMs total #putative promoters MCF7(Solexa) 11,919,330 10,000,349 12,133 29,210 HEK293(Solexa) 10,062,560 8,633,345 11,598 41,238 cDNA(Sanger, total) 1,540,411 1,370,985 15,194 32,122

Identification of the Putative Alternative Promoters (PAPs) in Human Genes Statistics of the Database

Figure 1. Identification of the Putative Alternative Promoters (PAPs) in Human Genes Schematic representation of the mapping of the 5'-ends of the oligo-cap cDNAs, the determination of the TSSs and clustering of the TSSs to identify the PAPs. The boxes and lines represent exons and introns, respectively. The RefSeq sequences and the oligo-cap cDNAs are colored in red and blue, respectively. The lowest gray oligo-cap cDNA is excluded from the dataset, since its 5'-end is located within an internal exon of the RefSeq. The third-lowest oligo-cap cDNA is accepted because the truncation of the erroneously sliced second-lowest transcript would otherwise need to be hypothesized to explain its presence, and the chance of the combination of such events should be low. The shaded boxes represent the retained introns. Altogether, this case consists of 8 "full-length" oligo-cap cDNAs that are mapped at 6 TSSs, clustered into 3 PAPs.

Statistics of the Putative Alternative Promoters (PAPs) Statistics of the Database

Table 3. Statistics of the Putative Alternative Promoters (PAPs) #PAPs #Locus #included TSS positions #cDNA clones(ave.) 1(PAP-less) 6954 (48%) 70175 43 2 3724 (26%) 67846 83 3 1821 (12%) 44455 115 4 1003 (6.9%) 32582 160 5 490 (3.3%) 19962 166 6 294 (2.0%) 13937 159 7 147 (1.0%) 7948 184 8 85 (0.6%) 4912 194 9 42 (0.3%) 2167 163 10 25 (0.2%) 1650 164 >10 43 (0.3%) 4140 341 total 14628 (100%) 269774 80

Schematic representation of the data flow Statistics of the Database

Figure 2. Schematic representation of the data flow The boxes that are marked with asterisks (A~G*) correspond to the respective forms illustrated in Figure XXX.

classification of the TSSs using different cut-offs and criteria Statistics of the Database

Figure 3. classification of the TSSs using different cut-offs and criteria The distribution of the putative alternative promoters (PAPs) was calculated using different intervals. The vertical axis shows the number of the AP containing genes. The horizontal axis represents the intervals separating the PAPs.

Size of the one TSS cluster Statistics of the Database

Figure 4. Size of the one TSS cluster The horizontal axis shows the size of the TSS clusters (distance between the two TSSs the farthest apart). The vertical axis shows the number of clusters.

<<Back