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Microarray: mRNA, Exon, Non-coding RNA, ChIP-chip

Our ability to focus on the original scientific goals of scientists much more efficiently comes from our original research interest and experience in the domain. Combining the computational expertise with biocuration, the team has developed more efficient gene expression databases as well as new software - including a few for the downstream functional analysis (see our publications and Startbioinfo). We also invented highly promising new ways to perform integrated analysis of multiple types of gene expression data, across techniques/platforms, thereby making an efficient use of public data while analyzing new data - both in terms of identifying molecular mechanisms of interest as well as biomarkers.

Gene expression array
Illustrative list of tasks
  • Pre-processing
  • Data normalization
  • Differential gene expression
  • Statistical analysis
  • Functional analysis: Gene Ontology, Pathways
  • Advanced functional analysis: Transcription factor binding site analysis, Protein-interaction networks, Promoter analysis, Domains, miRNA targets (for miRNA microarray)
  • Report with publication quality tables and figures
Example(s) of completed projects
  • Microarray analysis of cancer associated fibroblasts from cervical cancer for a research group at KMIO, India.
  • miRNA analysis and target prediction of a rodent species for a research group at CCMB, Hyderabad, India.
  • Exon array analysis and annotation of a rodent species for a research group at CCMB, Hyderabad, India.
  • Cancer data analysis of human genes for a research group at NIRRH, Mumbai, India.
  • Transcription regulatory network analysis of human genes for a research group at NIRRH, Mumbai, India.
  • Functional annotation and pathway analysis of infertility related human genes for a research group at NIRRH, Mumbai, India.
Relevant publications
  • Tumour Biol. 2016 Apr;37(4):4409-20
  • Fertil Steril. 2014 Jan;101(1):95-104.e3.
  • PLoS One. 2013;8(3):e58419.
  • BMC Genomics, [2013] 14: 922
  • PLoS One. 2012, 7(5), e36776
  • BMC Genomics. 2010, 11: 467
In house research
  • An algorithm developed for integrated analysis and ranking of most important genes in specific contexts.
  • Multiple mammalian gene expression databases developed using biocurated data.
  • A platform developed for obtaining transcript level data using existing microarray gene expression profiles.
  • Compilation of gene expression resources and their features (www.startbioinfo.com)

ChIP-chip (ChIP-microarray)
Illustrative list of tasks
  • Quality analysis
  • Normalization
  • Statistical analysis to explore ChIP enrichment and sample correlation
  • Peak calling/Enriched binding regions and Visualization
  • Identification of differential peaks/binding regions
  • Annotation of nearest Transcriptional start site/TSS
  • Functional analysis of differentially enriched genes
  • Report with publication quality tables and figures
Example(s) of completed projects
  • ChIP-Seq/ChIP-chip data analysis of mouse brain samples, for a research group at CCMB, Hyderabad, India.
  • ChIP-Seq data analysis for a research group at KMIO, Bengaluru, India.
In house research

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