PROMO: detection of known transcription regulatory elements
  using species-tailored searches

Messeguer, Xavier; Escudero, Ruth; Farré, Domènec; Núñez, Óscar; Martínez, Javier González; Albà, M. Mar

doi:10.1093/bioinformatics/18.2.333

Cited by 1,196 publications

(948 citation statements)

References 7 publications

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“…The promoter region of PRKD1 was analysed using two software programs (BDGP Neural Network promoter prediction software, http://www.fruitfly.org/seq_tools/ promoter.html 27 and Promo 3.0, http://alggen.lsi.upc.es/cgi-bin/ promo_v3/promo/promoinit.cgi?dirDB=TF_8.3 ). 28 There were no differences between the predictions from the wild-type sequence and Figure 1 14q12 microdeletions excluding coding region of FOXG1. Microdeletions at 14q12 were detected in three patients in this report (cases 1-3) by array CGH.…”

Section: Chromosomal Microarray Analysismentioning

confidence: 88%

14q12 microdeletions excluding FOXG1 give rise to a congenital variant Rett syndrome-like phenotype

Ellaway

Bettella

et al. 2012

Eur J Hum Genet

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Rett syndrome is a clinically defined neurodevelopmental disorder almost exclusively affecting females. Usually sporadic, Rett syndrome is caused by mutations in the X-linked MECP2 gene in B90-95% of classic cases and 40-60% of individuals with atypical Rett syndrome. Mutations in the CDKL5 gene have been associated with the early-onset seizure variant of Rett syndrome and mutations in FOXG1 have been associated with the congenital Rett syndrome variant. We report the clinical features and array CGH findings of three atypical Rett syndrome patients who had severe intellectual impairment, early-onset developmental delay, postnatal microcephaly and hypotonia. In addition, the females had a seizure disorder, agenesis of the corpus callosum and subtle dysmorphism. All three were found to have an interstitial deletion of 14q12. The deleted region in common included the PRKD1 gene but not the FOXG1 gene. Gene expression analysis suggested a decrease in FOXG1 levels in two of the patients. Screening of 32 atypical Rett syndrome patients did not identify any pathogenic mutations in the PRKD1 gene, although a previously reported frameshift mutation affecting FOXG1 (c.256dupC, p.Gln86ProfsX35) was identified in a patient with the congenital Rett syndrome variant. There is phenotypic overlap between congenital Rett syndrome variants with FOXG1 mutations and the clinical presentation of our three patients with this 14q12 microdeletion, not encompassing the FOXG1 gene. We propose that the primary defect in these patients is misregulation of the FOXG1 gene rather than a primary abnormality of PRKD1.

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Section: Chromosomal Microarray Analysismentioning

confidence: 88%

14q12 microdeletions excluding FOXG1 give rise to a congenital variant Rett syndrome-like phenotype

Ellaway

Bettella

et al. 2012

Eur J Hum Genet

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“…Our data suggest that SNPs in Haplotype 1 alter the binding of transcription factors which promote PMCA4b protein expression in myeloid blood cell differentiation, thus in RBC generation. Based on the PROMO (Alggen, [20]) database, the SNPs in Haplotype 1 may alter the binding sites for a large number of transcription factors, including GATA-1 and c-Myb, preferentially expressed in hematopoietic lineages. Further detailed studies are required to examine the role of the actual transcription factor binding sites in this region to regulate PMCA4 expression.…”

Section: Discussionmentioning

confidence: 99%

Decreased calcium pump expression in human erythrocytes is connected to a minor haplotype in the ATP2B4 gene

et al. 2017

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a b s t r a c tPlasma membrane Ca 2+ -ATPases are key calcium exporter proteins in most tissues, and PMCA4b is the main calcium transporter in the human red blood cells (RBCs). In order to assess the expression level of PMCA4b, we have developed a flow cytometry and specific antibody binding method to quantitatively detect this protein in the erythrocyte membrane. Interestingly, we found several healthy volunteers showing significantly reduced expression of RBC-PMCA4b. Western blot analysis of isolated RBC membranes confirmed this observation, and indicated that there are no compensatory alterations in other PMCA isoforms. In addition, reduced PMCA4b levels correlated with a lower calcium extrusion capacity in these erythrocytes. When exploring the potential genetic background of the reduced PMCA4b levels, we found no missense mutations in the ATP2B4 coding regions, while a formerly unrecognized minor haplotype in the predicted second promoter region closely correlated with lower erythrocyte PMCA4b protein levels. In recent GWA studies, SNPs in this ATP2B4 haplotype have been linked to reduced mean corpuscular hemoglobin concentrations (MCHC), and to protection against malaria infection. Our data suggest that an altered regulation of gene expression is responsible for the reduced RBC-PMCA4b levels that is probably linked to the development of human disease-related phenotypes.

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“…31 Putative binding sites for transcription factors were identified using PROMO 3.0, a web-based program that employs the TRANSFAC database version 8.3 to construct specific binding-site weight matrices for prediction of transcription factor-binding sites. 32,33 Relative telomere length assessment…”

Section: Spainmentioning

confidence: 99%

Genetic variant in the telomerase gene modifies cancer risk in Lynch syndrome

et al. 2012

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Lynch syndrome (LS) is an inherited cancer-predisposing disorder caused by germline mutations in the mismatch repair (MMR) genes. The high variability in individual cancer risk observed among LS patients suggests the existence of modifying factors. Identifying genetic modifiers of risk could help implement personalized surveillance programs based on predicted cancer risks. Here we evaluate the role of the telomerase (hTERT) rs2075786 SNP as a cancer-risk modifier in LS, studying 255 and 675 MMR gene mutation carriers from Spain and the Netherlands, respectively. The study of the Spanish sample revealed that the minor allele (A) confers increased cancer risk at an early age. The analysis of the Dutch sample confirmed the association of the A allele, especially in homozygosity, with increased cancer risk in mutation carriers under the age of 45 (relative risk LScao45_AA ¼ 2.90; 95% confidence interval ¼ 1.02-8.26). Rs2075786 is associated with colorectal cancer (CRC) risk neither in the general population nor in non-Lynch CRC families. In silico studies predicted that the SNP causes the disruption of a transcription binding site for a retinoid receptor, retinoid X receptor alpha, probably causing early telomerase activation and therefore accelerated carcinogenesis. Notably, cancer-affected LS patients with the AA genotype have shorter telomeres than those with GG. In conclusion, MMR gene mutation carriers with hTERT rs2075786 are at high risk to develop a LS-related tumor at an early age. Cancer-preventive measures and stricter cancer surveillance at early ages might help prevent or early detect cancer in these mutation carriers.

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PROMO: detection of known transcription regulatory elements using species-tailored searches

Abstract: We have developed a set of tools to construct positional weight matrices from known transcription factor binding sites in a species or taxon-specific manner, and to search for matches in DNA sequences.

Cited by 1,196 publications

References 7 publications

14q12 microdeletions excluding FOXG1 give rise to a congenital variant Rett syndrome-like phenotype

14q12 microdeletions excluding FOXG1 give rise to a congenital variant Rett syndrome-like phenotype

Decreased calcium pump expression in human erythrocytes is connected to a minor haplotype in the ATP2B4 gene

Genetic variant in the telomerase gene modifies cancer risk in Lynch syndrome

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