Documents

Subio製品・サービス紹介 [pdf, 日本語]

（株）Subioが提供する製品・サービスを紹介したパンフレットです。ご自由にお使いください。

Getting Started Guide [pdf, Engligh]

This is for who have not ever used Subio Platform or who just want to see data. It describes how to use Analysis Browser.

Getting Started Guide [pdf, 日本語]

はじめてご利用になる方は、まずこの資料をご参照ください。データを閲覧する操作についての説明があります。

Data Import and Analysis Guide [pdf, Engligh]

This is for who use Subio Basic Plug-in to anlayze their own data. It describes how to import data, edit information and use analysis tools.

Movies: Data Import

Import Subio Series Archive (ssa) Files. [movie, English]

Ssa files contain all information to reconstruct all analysis results. It's the easiest way to share omics data within team or with partners.

Import Affymetrix 3' IVT Expression Data [movie, English]

Instruction of importing Affymetrix 3' IVT expression microarray data.

Import Affymetrix Whole-Transcript Expression Data [movie, English]

Instruction of importing Affymetrix whole-transcript expression microarray data.

Import NimbleGen Expression Data [movie, English]

Instruction of importing NimbleGen expression microarray data.

Import Agilent Expression Microarray Data [movie, English]

Instruction of importing Agilent expression microarray data.

Import Agilent 2 color (dye-swap) Microarray Data [movie, English]

Instruction of importing 2 color (dye-swap) microarray data.

Import Agilent CGH Array Data [movie, English]

Instruction of importing Agilent CGH array data.

Import ChIP-Seq Data [movie, English]

Instruction of importing ChIP-Seq data based on next generation sequencing technologies.

Import GEO Data [movie, English]

Instruction of importing oimcs data which are freely available from GEO database.

Movies: Visualizations

Line Graph [movie, English]

Drag on Line Graph to select genes, which are also selected in the annotation table below at a same time.

Scatter Plot (Measurements) [movie, English]

Compare data distribution of two samples. You can easily assign samples to axes by drag & drop.

Tree View [movie, English]

A tree view visualizes a result of hierarchical clustering. You can easily traverse nodes by navigation buttons.

Scatter Plot (Samples) [movie, English]

Scatter Plot (Samples) visualizes a result of PCA. Colors of spots and arrows help your understanding.

Genomve View [movie, English]

You can visualize and search genomic location associated data like ChIP-chip/-seq, CGH and tiling array.

Movies: Analysis

Venn Diagram [movie, English]

Drag & drop a Measurement List on circles, then click area of extracting genes.

Normalization [movie, English]

Coordinate blocks to define normalization. You can promptly recall a saved normalization scheme.

Filtering [movie, English]

You can filter out genes by flag or signal values to remove noise disturbing statistical analysis.

Find Similar Pattern [movie, English]

You can extract genes which are correlated or anti-correlated to a template pattern.

Differential Expression Analysis [movie, English]

You can extract DEG (Differentially Expressed Genes) by fold and/or p-value. P-values can be corrected by BH FDR.

ANOVA [movie, English]

You can extract genes which are differentially expressed among groups by ANOVA.

Clustering [movie, English]

Hierarchical clustering is useful to group genes and samples by gene expression profiles.

Principal Component Analysis (PCA) [movie, English]

PCA is useful to summarize expression profile, especially for researching pathology and diagnosis.

Genomic Location Filter [movie, English]

You can extract genes of upstream, downstream or overlapping from genes, probes or sequence tags.

Search Gene by Genpac Interaction DB [movie, English]

You can search interactions from a gene or gene set. A result is in a simple table so that you can save as Excel sheet.

GO Enrichment Analysis [movie, English]

Gene Ontology analysis is very popular to characterize a gene set, which is extracted by a statistical analysis.

How to define web links [movie, English]

You can easily define web links by yourself, to get more information about genes.

Rスクリプトを使った統計処理 [movie, 日本語]

東大農学部　門田先生のRスクリプトで統計処理を実行する方法を解説しています。

Subio Platform Training Materials

Training Document [pdf, Engligh]

Please download before training by yourself, and print out if you need.

Demonstration data [zip, data]

Please download before training by yourself.