Consinspector 3.0: new library and enhanced functionality

Frech, Kornelie; Dietze, Peter; Werner, Thomas

doi:10.1093/bioinformatics/13.1.109

Cited by 6 publications

(4 citation statements)

References 10 publications

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“…The C/T + T/T variation was also observed as a somatic change only in the tumour tissue in 6/26 sporadic breast cancer patients (23%), conferring a possible risk to individuals with these genotypes either as a germline variant or as an acquired somatic change in a potential regulatory region. Further, a preliminary comparative analysis of the promoter region at −1349, performed using the ConsInspector 3.0 program (Frech et al ., 1993, 1997), revealed that the mutated sequence created an additional putative binding site for transcription factor GABP by changing the sequence from GGGA to GGAA (in the complementary strand), which could play a role in the differential expression of the gene. GABP has been found to enhance the expression of interleukin (IL)‐2 (Avots et al ., 1997) and IL‐16 (Bannert et al ., 1999).…”

Section: Discussionmentioning

confidence: 99%

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Transforming growth factor‐β1 genotype in sporadic breast cancer patients from India: status of enhancer, promoter, 5′‐untranslated‐region and exon‐1 polymorphisms

Saha

Gupta

Bairwa

et al. 2004

European Journal of Immunogenetics

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Transforming growth factor beta (TGF-beta) is an example for a large and still-growing family of growth factors. TGF-beta1 is known to act both as a tumour suppressor and as a stimulator of tumour progression. This study examines the relationship amongst putative enhancer, promoter, 5'-untranslated-region (UTR) and exon-1 polymorphisms of the TGF-beta1 gene (region I from -1881 to -1613; region II from -1410 to -1123, and region III from -55 to +176, as per human genome organisation (HUGO) nomenclature) in 26 breast cancer patients and 97 healthy control subjects. The germline and somatic status of the four known polymorphisms was ascertained, and a significant difference was observed for the germline C/T and T/T genotype distribution between patients and controls in comparison to C/C genotypes at position -1349 (chi2 = 6.193; P = 0.009). In addition to the somatic variations observed for some of the regions studied, in 10/26 (38%) sporadic breast cancer cases, a novel somatic mutation in codon 47 of exon 1 (GenBank accession number AY059373) was also detected in tumour samples. The risk of cancer was found to be significant (OR = 4.525) for the -1349 C/T and T/T genotype background, suggesting that this genetic background may act as a risk factor for sporadic breast cancer.

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Section: Discussionmentioning

confidence: 99%

“…Preliminary comparative analysis of the promoter region at −1349 was performed using the ConsInspector 3.0 program (Frech et al ., 1993, 1997) to determine differences in the binding of various transcription factors between wild‐type and mutated sequences of region II of the TGF‐β1 gene.…”

Section: Methodsmentioning

confidence: 99%

Transforming growth factor‐β1 genotype in sporadic breast cancer patients from India: status of enhancer, promoter, 5′‐untranslated‐region and exon‐1 polymorphisms

Saha

Gupta

Bairwa

et al. 2004

European Journal of Immunogenetics

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“…The change observed did not exist in the blood sample and was a somatic change. Analysis with the ‘ConsInspector 3.0’ program (Frech et al ., 1993, 1997) depicted variations in the putative binding sites for transcription factors like GRE and NFκ‐B, when mutated sequence (Acc. no.…”

Section: Introductionmentioning

confidence: 99%

Two novel somatic mutations in the human interleukin 6 promoter region in a patient with sporadic breast cancer

Saha¹,

Bairwa²,

Ranjan³

et al. 2003

European Journal of Immunogenetics

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Two new single nucleotide mutations were observed within the promoter region of human interleukin-6 gene (IL-6) in the tumour sample of a patient with sporadic breast cancer, which was a somatic change. Both mutations, one at -125 (C > G) and the other at position -173 (G > T) from the translation start site, were transversions observed at new positions, not reported earlier. In addition to these two novel mutations in this patient, a known somatic polymorphism was also observed at position -174 (G > C) (from the transcription initiation site, redesignated as -236 from the translational initiation site as per the HUGO nomenclature). Further, a preliminary comparative analysis of the studied promoter region by the 'ConsInspector 3.0' program, where the mutated sequence (AF362378) was compared with the sequence existing in the database (Y00081), depicted the presence of the variations in putative binding sites for transcription factors such as glucocorticoid response element (GRE) and nuclear factor kappa-B (NFkappa-B), which could lead to differential expression of this gene.

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“…A huge number of methods have been developed so far to address this problem. The most widely used are the matrix methods (2-6) based on the evolutionarily conservative nucleotides of functional sites and used by various Internet-available tools for promoter and transcription factor binding site recognition, i.e., object-oriented Transcription Factors Database (ooTFD) (7), PromFD (6), TESS (8), the TRANSFAC-based expert system (9), ConsInd and Cons-Inspector (10), MatInd and MatInspector (4), CoreSearch (11), MATRIX SEARCH (12), SIGNAL SCAN (13), FunSiteP (14), etc. These programs refer to consensuses and weight matrices for DNA-protein binding sites accumulated in the specialized databases such as TRANSFAC (9), IMD (12), RegulonDB (15), PLACE (16), PlantCARE (17), etc.…”

Section: Introductionmentioning

confidence: 99%

SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation

Ponomarenko

Orlova

Пономаренко

et al. 2000

Nucleic Acids Research

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SELEX_DB is a novel curated database on selected randomized DNA/RNA sequences designed for accumulation of experimental data on functional site sequences obtained by using SELEX and SELEX-like technologies from the pools of random sequences. This database also contains the programs for DNA/RNA functional site recognition within arbitrary nucleotide sequences. The first release of SELEX_DB has been installed under SRS and is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/systems/selex/

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Consinspector 3.0: new library and enhanced functionality

Cited by 6 publications

References 10 publications

Transforming growth factor‐β1 genotype in sporadic breast cancer patients from India: status of enhancer, promoter, 5′‐untranslated‐region and exon‐1 polymorphisms

Transforming growth factor‐β1 genotype in sporadic breast cancer patients from India: status of enhancer, promoter, 5′‐untranslated‐region and exon‐1 polymorphisms

Two novel somatic mutations in the human interleukin 6 promoter region in a patient with sporadic breast cancer

SELEX_DB: an activated database on selected randomized DNA/RNA sequences addressed to genomic sequence annotation

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