RGSiteScan program

Aim:

This program is designed to predict the potential binding sites of 37 transcription

factors, listed in Table below, in the target DNA sequence.

Limitations:

The current version of the program supposes the length of the target sequence to be limited by 32000bp.

Comments:

The prediction of binding sites of each transcription factor is performed

by means of the corresponding << Recognition Group >>.

All the 37 Recognition Groups are preliminary constructed by << RecGroup >> program.

The binding sites of 36 transcription factors (except for the case of TFIID)

are revealed in both strand orientations.

Table

The transcription binding sites scanned by RecGroupScan program with the corresponding type I and II errors. For denotation of the sites, see for example [1].

Boulikas, T. (1994). A compilation and classification of DNA-binding sites for protein transcription factors from vertebrates. Crit. Rev. Euk. Gene Express. 4, 117-321.

Note:

Only well represented sites (the training sample consists of more than 9 actual binding sites) have been assessed for the type I and II errors. In other cases, the cells are blank.

 

No

Binding sites

Type I error rate, a 1

Type II error rate, a 2

1)

AP1

0.188

0.004303

2)

AP2

0.125

0.000872

3)

APF

   

4)

AR

0.118

0.003092

5)

ATF/CREB

0.147

0.000207

6)

BPV-E2

   

7)

C/EBP

0.060

0.023392

8)

COUP/RAR

0.025

0.003936

9)

CP1

0.045

0.001466

10)

E2F

   

11)

E4F1

   

12)

E4TF1

   

13)

EF-C

   

14)

ETF

0.000

0.002229

15)

GATA

0.127

0.000491

16)

GT-2B

   

17)

GT-2C

   

18)

ICP4

   

19)

ICSBP

   

20)

IgPE-2

   

21)

MLTF

   

22)

NF-1

0.038

0.000620

23)

NFIII

   

24)

NF-kB

0.138

<10-5

25)

NF-uE1

   

26)

NF-uE3

   

27)

NF-uE4

   

28)

NF-uE5

   

29)

OCT

0.163

0.000505

30)

PEA1

   

31)

PEA2

   

32)

Pit-1

0.176

0.000522

33)

PU.1

   

34)

SIF

   

35)

Sp1

0.029

0.008347

36)

SRF

0.200

0.000029

37)

TFIID

   

 Algorithm designer >> Yury Kondrahin

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