We at Phalanx Biotech Group understand that navigating large genomic data sets can be daunting. Our team of highly-trained bioinformatics engineers will help you decipher your data. We’ve worked with clients across the academic and industry landscape in applications ranging from basic biology research to drug discovery. Whether you need us to run a complete analysis from raw data, or you need advanced analyses to answer specific questions, we’re here to help. We use validated analysis pipelines to give you quick answers to the most common questions, or we can build custom pipelines to meet your specific needs. Our Phalanx Biotech Group bioinformatics experts are eager to partner with you to translate your NGS or microarray data into breakthrough discoveries!

Next Generation Sequencing Data Analysis

The Phalanx Biotech Group bioinformatics team processes Illumina HiSeq, MiSeq, and NextSeq data using ready-made NGS pipelines which output standard and customized analysis packages. Please take a look at the content under each category for information on what kind of analyses we can provide. For customized NGS projects, please contact us to discuss what you’d like to see.

mRNA Sequencing (Gene Expression Analysis)

  • Data QC & filtering
  • Statistical analysis of differentially expressed genes
  • Gene Ontology and Pathway enrichment analysis
  • Principal components analysis

Small RNA Sequencing

  • Data QC & filtering
  • Analyze the expression pattern of known miRNAs
  • Identify novel miRNAs
  • Statistical analysis of differentially expressed miRNAs
  • Target prediction of novel and known miRNAs
  • Gene Ontology and Pathway enrichment analysis of miRNA target genes
  • Principal components analysis

Transcriptome De Novo Assembly

  • Data QC & filtering
  • Transcripts assembly
  • Known and novel transcript identification
  • Differential gene expression analysis
  • Gene Ontology and Pathway enrichment analysis
  • Principal components analysis
  • Novel lncRNA prediction
  • Differential lncRNA expression analysis
  • Up/down stream lncRNAs identified for specific genes
  • Pre-miRNA prediction

16S Metagenomics

  • Data QC & filtering
  • Number of raw reads, number of reads passing QC, number of Operational Taxonomic Units (OTUs)
  • Species composition and abundance analysis
  • Complexity of a single sample (alpha diversity)
  • Complexity differences between different samples (beta diversity, samples ≥ 2)
  • Principal component analysis (samples ≥ 3)
  • Clustering of species composition among samples (Samples ≥ 3)

ChIP-seq

  • Data QC & filtering
  • Align reads to the reference genome
  • Peak analysis (peak length and depth)
  • Peak annotation (peak distribution, Gene Ontology and Pathway analysis of peak related gene)
  • Identify differential peaks between samples
  • Differential peaks annotation (differential peaks distribution, GO and Pathway analysis of differential peak related gene)
  • Motif analysis

Whole Exome Sequencing

  • Data QC & filtering
  • Align reads to the human reference genome
  • SNP calling and annotation
  • SNP validation and comparison
  • Functional prediction of SNPs
  • InDel calling and annotation
  • InDel validation and comparison

Microarray Data Analysis

Our bioinformatics team has extensive experience working with microarray data from OneArray®, Affymetrix, Agilent, Illumina, and other platforms. Please take a look at the contents under each category for information on what kind of analyses we typically deliver. For custom projects, please submit a quote request and one of our microarray experts will follow up to discuss your project.

OneArray®

Our basic OneArray®data analysis package includes normalization, identification of differentially expressed genes, principal components analysis, hierarchical clustering, and Gene Ontology and Pathway enrichment analysis.

Agilent

Our basic Agilent data analysis package includes normalization, identification of differentially expressed genes, principal components analysis, and hierarchical clustering.

Affymetrix

Our basic Affymetrix data analysis package includes normalization, identification of differentially expressed genes, principal components analysis, and hierarchical clustering.

Illumina

Our basic Illumina data analysis package includes normalization, identification of differentially expressed genes, principal components analysis, and hierarchical clustering.

Advanced Analysis

  • Gene Ontology and Pathway enrichment analyses: using a set of differentially expressed genes, an enrichment analysis will find which GO terms and pathways are over-represented (or under-represented) using annotations for that gene set.
  • CMAP: a useful tool in the drug discovery process, OneArray® microarray results can be input into our CMAP pipeline in order to identify/predict the effects of different drugs on different compounds without having to run the wet lab experiments. Protein target prediction and advanced pathway analysis can be performed as subsequent analyses in order to give an even more complete picture of the experiment.

Advanced Analyses of Microarray or NGS Data

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Functional Analyses

Target gene prediction service, integrated analysis of mRNA and microRNA expression

Pattern Recognition

Heat map, unsupervised clustering analysis, functional clustering analysis, classification analysis

Visualization Analyses

Bar plot, box plot, volcano plot, Venn diagram, pie chart, principal components analysis 2D/3D plot, biological network data integration/analysis/visualization services

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