BATAGOV Arsen

A novel community driven software for functional enrichment analysis of extracellular vesicles data

Bioinformatics tools are imperative for the in depth analysis of heterogeneous high-throughput data. Most of the software tools are developed by specific laboratories or groups or companies wherein they are designed to perform the required analysis for the group. However, such software tools may fail to capture “what the community needs in a tool”. Here, we describe a novel community-driven approach to build a comprehensive functional enrichment analysis tool. Using the existing FunRich tool as a template, we invited researchers to request additional features and/or changes.

type: 
Journal Paper
journal: 
Journal of Extracellular Vesicles 2017, Vol. 6, 2017, Issue 1, doi: 10.1080/20013078.2017.1321455
Url: 
http://www.tandfonline.com/doi/abs/10.1080/20013078.2017.1321455
Impact Factor: 
4.259

Genome-wide analysis of mRNAs associated with mouse peroxisomes

Background: RNA is often targeted to be localized to the specific subcellular compartments. Specific localization of mRNA is believed to be an important mechanism for targeting their protein products to the locations, where their function is required.

type: 
Journal Paper
journal: 
BMC Genomics 2016, 17 (Supp 13), 1028, doi: 10.1186/s12864-016-3330-x
Url: 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5259856/
Impact Factor: 
3.869

Abstract 1990: The key role of MECOM complex locus and its products in high-grade ovarian carcinoma pathogenesis and clinical outcomes

The ecotropic virus integration site 1(Evi1) transcription factor, encoded in the MECOM complex locus, is implicated in several cancers, including ovarian cancer(OC). High-grade serous OC(HG-SOC) represents its most common and aggressive form. The pathobiological and clinical roles of MECOM and its products in HG-SOC are poorly understood.

type: 
Journal Paper
journal: 
Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA: Cancer Research Aug 1, 2015 75,1990, doi: 10.1158/1538-7445.AM2015-1990
Url: 
http://cancerres.aacrjournals.org/content/75/15_Supplement/1990

HOXD-AS1 is a novel lncRNA encoded in HOXD cluster and a marker of neuroblastoma progression revealed via integrative analysis of noncoding transcriptome

Background
Long noncoding RNAs (lncRNAs) constitute a major, but poorly characterized part of human transcriptome. Recent evidence indicates that many lncRNAs are involved in cancer and can be used as predictive and prognostic biomarkers. Significant fraction of lncRNAs is represented on widely used microarray platforms, however they have usually been ignored in cancer studies.

Results

type: 
Journal Paper
journal: 
BMC Genomics 2014, 15(Suppl 9):S7 doi:10.1186/1471-2164-15-S9-S7
Url: 
http://www.biomedcentral.com/1471-2164/15/S9/S7
Impact Factor: 
4.04

Role of genomic architecture in the expression dynamics of long noncoding RNAs during differentiation of human neuroblastoma cells

Background

type: 
Journal Paper
journal: 
BMC Systems Biology 2013, 7(Suppl 3):S11, doi:10.1186/1752-0509-7-S3-S11
Url: 
http://www.biomedcentral.com/1752-0509/7/S3/S11
Impact Factor: 
2.98

Exosomes secreted by human cells transport largely mRNA fragments that are enriched in the 3'-untranslated regions

Small secreted membrane vesicles called exosomes have recently attracted a great interest after the discovery that they transfer mRNA that can be translated into protein in recipient cells. Surprisingly, we found that for the majority of exosomal mRNAs only a fraction of their corresponding probes is detectable on the expression microarrays. Exosomal mRNA fragmentation is characterized with a specific structural pattern. The closer to the 3′-end of the transcript the fragments are localized, the larger fraction among the secreted RNAs they constitute.

type: 
Journal Paper
journal: 
Biology Direct 2013, 8:12, doi:10.1186/1745-6150-8-12
pubmed: 
23758897
Url: 
http://www.biology-direct.com/content/8/1/12
Impact Factor: 
2.72
Date of acceptance: 
2013-05-28

Beware Of Moving Targets: Reference Proteome Content Fluctuates Substantially Over The Years

Reference proteomes are generated by increasingly sophisticated annotation pipelines as part of regular genome build releases; yet, the corresponding changes in reference proteomes' content are dramatic. In the history of the NCBI-curated human proteome, the total number of entries has remained roughly constant but approximately half of the proteins from the 2003 build 33 are no longer represented by entries in current releases, while about the same number of new proteins have been added (for sequence identity thresholds 50-90%).

type: 
Journal Paper
journal: 
Journal of Bioinformatics and Computational Biology, Vol. 10, No. 6 (2012), doi: 10.1142/S0219720012500205
pubmed: 
22867629
Url: 
http://www.ncbi.nlm.nih.gov/pubmed/22867629
Date of acceptance: 
2012-09-15

Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic for FOS protein in invasive tumors

Ecotropic viral integration site 1 (EVI1) is an oncogenic dual domain zinc finger transcription factor that plays an essential role in the regulation of hematopoietic stem cell renewal, and its overexpression in myeloid leukemia and epithelial cancers is associated with poor patient survival. Despite the discovery of EVI1 in 1988 and its emerging role as a dominant oncogene in various types of cancer, few EVI1 target genes are known. This lack of knowledge has precluded a clear understanding of exactly how EVI1 contributes to cancer.

type: 
Journal Paper
journal: 
PNAS, 2012 Feb 7;109(6):2168-73. doi: 10.1073/pnas.1119229109
pubmed: 
22308434
Url: 
http://www.pnas.org/content/109/6/2168
Impact Factor: 
9.681

Ecotopic viral integration site 1 (EVI1) regulates multiple cellular processes important for cancer and is a synergistic for FOS protein in invasive tumors

Ecotropic viral integration site 1 (EVI1) is an oncogenic dual domain zinc finger transcription factor that plays an essential role in the regulation of hematopoietic stem cell renewal, and its overexpression in myeloid leukemia and epithelial cancers is associated with poor patient survival. Despite the discovery of EVI1 in 1988 and its emerging role as a dominant oncogene in various types of cancer, few EVI1 target genes are known. This lack of knowledge has precluded a clear understanding of exactly how EVI1 contributes to cancer.

type: 
Journal Paper
journal: 
PNAS, 2012 Feb 7;109(6):2168-73. doi: 10.1073/pnas.1119229109
pubmed: 
22308434
Url: 
http://www.pnas.org/content/109/6/2168
Impact Factor: 
9.681

Identification of nucleotide patterns enriched in secreted RNAs as putative cis-acting elements targeting them to exosome nano-vesicles

Background

Exosomes are nanoscale membrane vesicles released by most cells. They are postulated to be involved in cell–cell communication and genetic reprogramming of their target cells. In addition to proteins and lipids, they release RNA molecules many of which are not present in the donor cells implying a highly selective mode of their packaging into these vesicles. Sequence motifs targeting RNA to the vesicles are currently unknown.
Results

type: 
Journal Paper
journal: 
BMC Genomics 2011, Vol. 12 (Suppl 3):S18
Url: 
http://www.biomedcentral.com/content/pdf/1471-2164-12-S3-S18.pdf
Impact Factor: 
3.99
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