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Umer, Husen Muhammad
Publications (3 of 3) Show all publications
Diamanti, K., Umer, H. M., Kruczyk, M., Dabrowski, M. J., Cavalli, M., Wadelius, C. & Komorowski, J. (2016). Maps of context-dependent putative regulatory regions and genomic signal interactions. Nucleic Acids Research, 44(19), 9110-9120.
Open this publication in new window or tab >>Maps of context-dependent putative regulatory regions and genomic signal interactions
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2016 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 44, no 19, 9110-9120 p.Article in journal (Refereed) Published
Abstract [en]

Gene transcription is regulated mainly by transcription factors (TFs). ENCODE and Roadmap Epigenomics provide global binding profiles of TFs, which can be used to identify regulatory regions. To this end we implemented a method to systematically construct cell-type and species-specific maps of regulatory regions and TF-TF interactions. We illustrated the approach by developing maps for five human cell-lines and two other species. We detected similar to 144k putative regulatory regions among the human cell-lines, with the majority of them being similar to 300 bp. We found similar to 20k putative regulatory elements in the ENCODE heterochromatic domains suggesting a large regulatory potential in the regions presumed transcriptionally silent. Among the most significant TF interactions identified in the heterochromatic regions were CTCF and the cohesin complex, which is in agreement with previous reports. Finally, we investigated the enrichment of the obtained putative regulatory regions in the 3D chromatin domains. More than 90% of the regions were discovered in the 3D contacting domains. We found a significant enrichment of GWAS SNPs in the putative regulatory regions. These significant enrichments provide evidence that the regulatory regions play a crucial role in the genomic structural stability. Additionally, we generated maps of putative regulatory regions for prostate and colorectal cancer human cell-lines.

National Category
Biochemistry and Molecular Biology
Identifiers
urn:nbn:se:uu:diva-310761 (URN)10.1093/nar/gkw800 (DOI)000388016900012 ()27625394 (PubMedID)
Funder
AstraZenecaSwedish Research CouncilSwedish Diabetes AssociationeSSENCE - An eScience Collaboration
Note

De två första författarna delar förstaförfattarskapet.

Available from: 2016-12-19 Created: 2016-12-19 Last updated: 2017-11-29Bibliographically approved
Dabrowski, M., Pilot, M., Kruczyk, M., Zmihorski, M., Umer, H. M. & Gliwicz, J. (2014). Reliability assessment of null allele detection: inconsistencies between and within different methods. Molecular Ecology Resources, 14(2), 361-373.
Open this publication in new window or tab >>Reliability assessment of null allele detection: inconsistencies between and within different methods
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2014 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 14, no 2, 361-373 p.Article in journal (Refereed) Published
Abstract [en]

Microsatellite loci are widely used in population genetic studies, but the presence of null alleles may lead to biased results. Here, we assessed five methods that indirectly detect null alleles and found large inconsistencies among them. Our analysis was based on 20 microsatellite loci genotyped in a natural population of Microtus oeconomus sampled during 8years, together with 1200 simulated populations without null alleles, but experiencing bottlenecks of varying duration and intensity, and 120 simulated populations with known null alleles. In the natural population, 29% of positive results were consistent between the methods in pairwise comparisons, and in the simulated data set, this proportion was 14%. The positive results were also inconsistent between different years in the natural population. In the null-allele-free simulated data set, the number of false positives increased with increased bottleneck intensity and duration. We also found a low concordance in null allele detection between the original simulated populations and their 20% random subsets. In the populations simulated to include null alleles, between 22% and 42% of true null alleles remained undetected, which highlighted that detection errors are not restricted to false positives. None of the evaluated methods clearly outperformed the others when both false-positive and false-negative rates were considered. Accepting only the positive results consistent between at least two methods should considerably reduce the false-positive rate, but this approach may increase the false-negative rate. Our study demonstrates the need for novel null allele detection methods that could be reliably applied to natural populations.

Keyword
heterozygosity, bottleneck, microsatellite loci, genotyping errors, null alleles, Microtus oeconomus
National Category
Natural Sciences
Identifiers
urn:nbn:se:uu:diva-220981 (URN)10.1111/1755-0998.12177 (DOI)000331469500013 ()
Available from: 2014-03-25 Created: 2014-03-24 Last updated: 2017-12-05Bibliographically approved
Kruczyk, M., Umer, H. M., Enroth, S. & Komorowski, J. (2013). Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data. BMC Bioinformatics, 14, 280.
Open this publication in new window or tab >>Peak Finder Metaserver - a novel application for finding peaks in ChIP-seq data
2013 (English)In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 14, 280- p.Article in journal (Refereed) Published
Abstract [en]

Background: Finding peaks in ChIP-seq is an important process in biological inference. In some cases, such as positioning nucleosomes with specific histone modifications or finding transcription factor binding specificities, the precision of the detected peak plays a significant role. There are several applications for finding peaks (called peak finders) based on different algorithms (e.g. MACS, Erange and HPeak). Benchmark studies have shown that the existing peak finders identify different peaks for the same dataset and it is not known which one is the most accurate. We present the first meta-server called Peak Finder MetaServer (PFMS) that collects results from several peak finders and produces consensus peaks. Our application accepts three standard ChIP-seq data formats: BED, BAM, and SAM. Results: Sensitivity and specificity of seven widely used peak finders were examined. For the experiments we used three previously studied Transcription Factors (TF) ChIP-seq datasets and identified three of the selected peak finders that returned results with high specificity and very good sensitivity compared to the remaining four. We also ran PFMS using the three selected peak finders on the same TF datasets and achieved higher specificity and sensitivity than the peak finders individually. Conclusions: We show that combining outputs from up to seven peak finders yields better results than individual peak finders. In addition, three of the seven peak finders outperform the remaining four, and running PFMS with these three returns even more accurate results. Another added value of PFMS is a separate report of the peaks returned by each of the included peak finders.

Keyword
Transcription factor, Peak finder, ChIP-seq, Metaserver
National Category
Medical and Health Sciences
Identifiers
urn:nbn:se:uu:diva-213840 (URN)10.1186/1471-2105-14-280 (DOI)000327524600002 ()
Available from: 2014-01-05 Created: 2014-01-04 Last updated: 2017-12-06Bibliographically approved
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