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Zamani, Neda
Publications (4 of 4) Show all publications
Moghadam, B. T., Zamani, N., Komorowski, J. & Grabherr, M. (2017). PiiL: visualization of DNA methylation and gene expression data in gene pathways. BMC Genomics, 18, Article ID 571.
Open this publication in new window or tab >>PiiL: visualization of DNA methylation and gene expression data in gene pathways
2017 (English)In: BMC Genomics, E-ISSN 1471-2164, Vol. 18, article id 571Article in journal (Refereed) Published
Abstract [en]

Background: DNA methylation is a major mechanism involved in the epigenetic state of a cell. It has been observed that the methylation status of certain CpG sites close to or within a gene can directly affect its expression, either by silencing or, in some cases, up-regulating transcription. However, a vertebrate genome contains millions of CpG sites, all of which are potential targets for methylation, and the specific effects of most sites have not been characterized to date. To study the complex interplay between methylation status, cellular programs, and the resulting phenotypes, we present PiiL, an interactive gene expression pathway browser, facilitating analyses through an integrated view of methylation and expression on multiple levels.

Results: PiiL allows for specific hypothesis testing by quickly assessing pathways or gene networks, where the data is projected onto pathways that can be downloaded directly from the online KEGG database. PiiL provides a comprehensive set of analysis features that allow for quick and specific pattern searches. Individual CpG sites and their impact on host gene expression, as well as the impact on other genes present in the regulatory network, can be examined. To exemplify the power of this approach, we analyzed two types of brain tumors, Glioblastoma multiform and lower grade gliomas.

Conclusion: At a glance, we could confirm earlier findings that the predominant methylation and expression patterns separate perfectly by mutations in the IDH genes, rather than by histology. We could also infer the IDH mutation status for samples for which the genotype was not known. By applying different filtering methods, we show that a subset of CpG sites exhibits consistent methylation patterns, and that the status of sites affect the expression of key regulator genes, as well as other genes located downstream in the same pathways.

PiiL is implemented in Java with focus on a user-friendly graphical interface. The source code is available under the GPL license from https://github.com/behroozt/PiiL.git.

Keywords
DNA methylation, Gene expression, Visualization, KEGG pathways
National Category
Medical Biotechnology
Identifiers
urn:nbn:se:umu:diva-138678 (URN)10.1186/s12864-017-3950-9 (DOI)000406759000002 ()28768481 (PubMedID)2-s2.0-85026625868 (Scopus ID)
Available from: 2017-08-30 Created: 2017-08-30 Last updated: 2024-01-17Bibliographically approved
Lamichhaney, S., Berglund, J., Almen, M. S., Maqbool, K., Grabherr, M., Martinez-Barrio, A., . . . Andersson, L. (2015). Evolution of Darwin's finches and their beaks revealed by genome sequencing. Nature, 518(7539)
Open this publication in new window or tab >>Evolution of Darwin's finches and their beaks revealed by genome sequencing
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2015 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 518, no 7539Article in journal (Refereed) Published
Abstract [en]

Darwin's finches, inhabiting the Galapagos archipelago and Cocos Island, constitute an iconic model for studies of speciation and adaptive evolution. Here we report the results of whole-genome re-sequencing of 120 individuals representing all of the Darwin's finch species and two close relatives' Phylogenetic analysis reveals important discrepancies with the phenotype-based taxonomy. We find extensive evidence for interspecific gene flow throughout the radiation. Hybridization has given rise to species of mixed ancestry. A 240 kilobase haplotype encompassing the ALX1 gene that encodes a transcription factor affecting craniofacial. development is strongly associated with beak shape diversity across Darwin's finch species as well as within the medium ground finch (Geospiza fortis) a species that has undergone rapid evolution of beak shape in response to environmental changes. The ALX1 haplotype has contributed to diversification of beak shapes among the Darwin's finches and thereby, to an expanded utilization of food resources.

National Category
Botany
Identifiers
urn:nbn:se:umu:diva-100947 (URN)10.1038/nature14181 (DOI)000349547400036 ()25686609 (PubMedID)2-s2.0-84923353165 (Scopus ID)
Available from: 2015-03-23 Created: 2015-03-16 Last updated: 2023-03-23Bibliographically approved
Delhomme, N., Sundström, G., Zamani, N., Lantz, H., Lin, Y.-C., Hvidsten, T. R., . . . Street, N. R. (2015). Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). PLOS ONE, 10(9), Article ID e0139080.
Open this publication in new window or tab >>Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies)
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2015 (English)In: PLOS ONE, E-ISSN 1932-6203, Vol. 10, no 9, article id e0139080Article in journal (Refereed) Published
Abstract [en]

After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant's phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.

National Category
Biological Sciences
Identifiers
urn:nbn:se:umu:diva-110568 (URN)10.1371/journal.pone.0139080 (DOI)000362170700039 ()26413905 (PubMedID)2-s2.0-84946944594 (Scopus ID)
Available from: 2015-10-27 Created: 2015-10-23 Last updated: 2023-03-24Bibliographically approved
Sundstrom, G., Zamani, N., Grabherr, M. G. & Mauceli, E. (2015). Whiteboard: a framework for the programmatic visualization of complex biological analyses. Bioinformatics, 31(12), 2054-2055
Open this publication in new window or tab >>Whiteboard: a framework for the programmatic visualization of complex biological analyses
2015 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 31, no 12, p. 2054-2055Article in journal (Refereed) Published
Abstract [en]

A Summary: Whiteboard is a class library implemented in C++ that enables visualization to be tightly coupled with computation when analyzing large and complex datasets.

National Category
Bioinformatics and Systems Biology
Identifiers
urn:nbn:se:umu:diva-106566 (URN)10.1093/bioinformatics/btv078 (DOI)000356625700071 ()25661541 (PubMedID)2-s2.0-84931066106 (Scopus ID)
Available from: 2015-07-20 Created: 2015-07-20 Last updated: 2023-03-24Bibliographically approved
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