Genome Analysis Software Info Site

This is a function to map a probe to annotated nucleotide sequence file. 

You can read the probe file and map it to the origin position on the current genome sequence.

When there is position information on the genome, paste the probe feature to the corresponding genome position based on the position information of each probe.

If position information does not exist and only the base sequence of the probe is given, mapping is performed based on the homology of the probe base sequence.

Currently mappable probes belong to the following array makers.

• Affymetrix
• Agilent
• Nimblegen

This function can be executed with the following edition.

AE, DS, GT

Import tiling array expression data files and NGS RNA-Seq files so that they can be used for array expression analysis.

There is no limit on the number of expression data files that can be imported, but you can only import 10 files with one operation.

Probe mapping must be performed before this function can be executed.

You can load a genome base sequence file, map a probe file, import a expression data file, register it as a batch process, and execute it in the background.

The expression level for each probe can be displayed as a bar graph or a line graph on the array profile lane of the main feature map.

There is no limit on the number of lanes to display at the same time, but as you increase the number of lanes, it consumes more memory.

Any number of expression profile lanes can be displayed on the main feature map.

Also, you can move its position freely up and down.

Expression profiles belonging to that region are also inherited if genomic sequences with expression profiles are digested, truncated, amplified, ligated, etc. by cloning operation.

This function is installed in the following software edition

IMCAE, IMCDS, GenomeTraveler

On the expression profile lane you can perform the following operations.

• Setting lane style
• Import color data
• Clear color data
• Output CSV format file of expression profile
• Profile Magnified

This function corrects the expression profile data.

Data correction functions include the following.

• MM Subtraction from PM
• Quality Trimming
• Saturation Trimming
• Global Rank Trimming
• Global Rate Trimming
• Base Window Rank Trimming
• Probe Window Rank Trimming
• Probe Window Rate Trimming
• Border Line Trimming
• Base Window Rate Trimming
• R-I Conversion
• Level Conversion
• Trimmed Mean
• Trimmed Median

These data corrections are pipelined to execute multiple correction items in an arbitrary order.

The applied state of these data corrections is shown on the list displayed for each expression data file.

A statistical number of correction values ​​of the results of these data corrections can be displayed in a list for each expression data file.

The distribution of the expression levels before and after the data correction can be displayed in a graph.

This function can be executed with the following edition.

AE, DS, GT

Lengths of probes of tiling arrays are usually shorter than genes, and multiple probes are designed at approximately equal intervals on genes and between genes.

In addition, the measured primary data is the expression level for each probe.

Therefore, focusing on one gene, multiple probes and multiple expression levels can be obtained there.

This function converts the expression level of the probe placed on the gene into the expression level of the gene.

This function can be executed with the following edition.

AE, DS, GT

This function can be executed with the following edition.

AE, DS, GT

Detect peaks from the expression profile.

Detection results are listed in the Peak List dialog.

The list can be saved as a CSV file.

When you click on the list, the main feature map will automatically scroll so that its position is centered.

This function can be executed with the following edition.

AE, DS, GT

Plot the correlation of expression levels between arbitrary arrays.

• X-Y plot
• R-I plot

This function can be executed with the following edition.

AE, DS, GT

Clustering of gene expression levels.

Clustering results can be displayed as dendrograms and heat maps.

This function can be executed with the following edition.

AE, DS, GT

As for the presently imported expression level data file, the expression levels by feature are listed.

Features to display in the list dialog can be selected (multiple selections possible).

The list can be sorted with up to four sort keys per column.

This function is implemented in the following edition.

AE, DS, GT