Bioinformatics

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

我們的生物資訊學團隊在處理OneArray®、Affymetrix、Agilent，Illumina和其他平台的數據分析方面擁有豐富的經驗。請查看以下內容了解我們可以提供的分析類型。

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