STATISTICS

General Total Number of Entries Table Release 11.1 Release 12.1 Factor, total 9,621 11,080    transcription factors 9,380 10,843    miRNA 241 237 Site, total 19,114 21,620    DNA sites 18,762 21,268    RNA sites 352 352 ChIP-chip fragment 16,884 141,595 Gene, total 24,681 32,296 Gene, linked1 19,338 26,709 Matrix 821 846 Cell 2,393 3,120 Class 57 57 Method 115 115 Reference 14,783 16,862 1genes that are linked to site, ChIP-chip fragment and/or factor

Factor Number of Entries Entries discriminated by taxa1 Release 11.1 Release 12.1 Vertebrata 5,242 6,231    Homo sapiens 2,006 2,373 Insecta 379 382 Plants 3,229 3,660 Fungi 485 538    S. cerevisiae 370 402 Viridae 45 48 Nematoda 226 225 1The number of factors listed here exceeds the total number of factors because multi-species transcription factor complexes can add to the count in several taxa. Expression Patterns Number of Entries   Release 11.1 Release 12.1 Factors with expression patterns 420 424 Average number of expression patterns per factor 17 17 Cross-links to external databases (DB) Release 11.1 Release 12.1   Linked TRANSFAC entries Linked DB entries Links total number Linked TRANSFAC entries Linked DB entries Links total number EMBL 5,182 6,786 7,257 5,320 6,939 7,412 Swiss-Prot 5,599 4,563 5,762 6,414 4,754 6,606 PIR 1,148 1,371 1,445 1,149 1,372 1,445 FlyBase 181 153 188 181 153 188 PDB 71 92 147 101 118 201 DATF 1,470 1,440 1,470 1,526 1,440 1,526 Cross-links to BIOBASE databases (DB) Release 11.1 Release 12.1   Linked TRANSFAC entries Linked DB entries Links total number Linked TRANSFAC entries Linked DB entries Links total number PROTEOME 2,461 1,501 2,461 2,458 1,499 2,458 TRANSCompel® 315 409 975 330 420 1,049 S/MARt DBTM 27 27 27 31 31 31 PathoDB® 58 10,896 10,896 58 10,896 10,896 TRANSPATH® 5,932 5,932 5,932 6,905 6,905 6,905 Factor Superclass Release 11.1 Release 12.1   Entries Linked Sites Linked Matrices Entries Linked Sites Linked Matrices I. Basic Domains 1,014 4,057 1,100 1,149 4,607 1,185 II. Zinc- coordinating DNA- binding domains 1,204 6,573 872 1,299 7,519 924 III. Helix-turn-helix 2,262 6,597 1,094 2,485 6,953 1,133 IV. beta-Scaffold Factors with Minor Groove Contacts 324 1,375 257 353 1,532 268 V. Other Transcription Factors 396 1,314 250 450 1,397 262 Class assignments 5,200 19,916 3,573 5,736 22,008 3,772 Unclassified 4,180 3,975 376 5,107 5,505 417 miRNA 241 449 - 237 449 - Total 9,621 24,340 3,949 11,080 27,962 4,189 The number of linked sites exceeds the total number of site entries, because more than one factor can be linked to one site. Also, orthologous factors can be linked to one matrix, resulting in a higher number of factor-matrix-links.

Site Number of Entries Entries discriminated by taxa Release 11.1 Release 12.1 Vertebrata 6,562 8,233    Homo sapiens 2,976 3,899 Insecta 1,405 1,409 Plants 719 852 Fungi 653 832    S. cerevisiae 531 675 Viridae 722 727 Other 93 101   Artificial 8,500 9,008 Consensi 460 458 Sequences Number of Entries   Release 11.1 Release 12.1 Sequences 18,656 21,075 Nucleotides 405,079 474,265 Cross-links to external databases (DB) Release 11.1 Release 12.1   Linked TRANSFAC entries Linked DB entries Links total number Linked TRANSFAC entries Linked DB entries Links total number EMBL 6,641 2,617 7,831 8,013 3,179 9,208 EPD 936 244 1,129 936 244 1,129 FlyBase 381 51 384 381 51 384 Cross-links to TRANSFAC System databases (DB) Release 11.1 Release 12.1   Linked TRANSFAC entries Linked DB entries Links total number Linked TRANSFAC entries Linked DB entries Links total number TRANSCompel® 74 46 86 72 45 84 PathoDB® 7 16 16 7 16 16 TRANSPRO® 3,431 1,734 6,192 4,330 2,044 7,164

Gene Number of Entries Entries discriminated by taxa1) Release 11.1 Release 12.1 Vertebrata 17,269 24,450    Homo Sapiens 11,086 17,993 Insecta 209 210 Plants 1,140 1,333 Fungi 611 680    S. cerevisiae 550 589 Viridae 92 92 Cross-links to external databases2) (DB) Release 11.1 Release 12.1   Linked TRANSFAC entries Linked DB entries Links total number Linked TRANSFAC entries Linked DB entries Links total number Affymetrix 19,567 160,362 168,603 26,318 126,303 160,928 EMBL 21,678 181,738 194,537 28,832 226,874 262,745 Ensembl 19,623 19,627 19,629 26,809 26,807 26,809 BRENDA 311 267 323 310 267 322 ENTREZ GENE 22,029 22,027 22,029 29,665 29,663 29,665 HGNC 11,451 11,452 11,452 17,287 17,288 17,288 MGI 6,978 8,901 8,965 7,618 16,150 16,247 OMIM 8,434 10,034 10,554 11,739 13,932 15,379 REFSEQ 20,133 63,926 64,725 27,263 83,781 85,138 RGD 1,744 1,979 1,986 2,435 4,934 4,954 UniGene 20,857 34,100 34,978 27,844 48,368 49,887 Cross-links to BIOBASE databases2) (DB) Release 11.1 Release 12.1   Linked TRANSFAC entries Linked DB entries Links total number Linked TRANSFAC entries Linked DB entries Links total number Proteome 15,141 14,416 15,141 15,125 14,400 15,125 TRANSPATH® 11,546 11,546 11,546 15,767 15,767 15,767 TRANSCompel® 283 417 417 283 417 417 TRANSProTM 20,607 56,099 56,099 22,378 50,546 50,546 PathoDB® 7 16 16 7 16 16 S/MARt DBTM 212 324 490 230 363 530 1) only gene entries that are linked to site, ChIP-chip fragment and/or factor were counted 2) all gene entries were counted

Matrix Number of Entries Entries discriminated by taxa Release 11.1 Release 12.1 Vertebrata 588 610 Insecta 67 67 Plants 102 104 Fungi 56 57 Nematoda 7 7 Prokaryota 1 1

Cell   Cross-links to external databases (DB) Release 11.1 Release 12.1   Linked TRANSFAC entries Linked DB entries Links total number Linked TRANSFAC entries Linked DB entries Links total number CLDB 197 247 252 200 254 254

Class   Cross-links to external databases (DB) Release 11.1 Release 12.1   Linked TRANSFAC entries Linked DB entries Links total number Linked TRANSFAC entries Linked DB entries Links total number PROSITE 26 24 35 26 24 35