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Integration method for gene expression data by crossing chip platforms

A gene expression and data integration technology, which is applied in the fields of digital data processing, special data processing applications, instruments, etc., can solve the problem of no standardization of median and variance between data samples, no consideration of different linear proportions of genes, and unfavorable comparison between data. And other issues

Active Publication Date: 2014-04-23
艾吉泰康(嘉兴)生物科技有限公司
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  • Claims
  • Application Information

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Problems solved by technology

The above algorithm has the following disadvantages: 1) The chip preprocessing method is very important for the subsequent analysis, only the log2 transformation is used and the background correction method is ignored; 2) When evaluating the linear relationship between gene expression between the two platforms, Only the maximum expression value of the chip is considered, but the linear ratio of the gene in different segments is not considered; 3) The median and variance between samples are not standardized, which is not conducive to the comparison between data

Method used

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  • Integration method for gene expression data by crossing chip platforms
  • Integration method for gene expression data by crossing chip platforms
  • Integration method for gene expression data by crossing chip platforms

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Embodiment 1

[0061] Example 1. In order to evaluate the difference in gene expression between different chip platforms and realize the cross-platform integration of gene expression data, 10 cases of breast cancer tissue samples and 10 cases of normal paracancerous tissues were detected by Affymetrix HG U133A and Agilent G4112F chip platforms respectively Gene expression of samples.

[0062] (1), Affymetrix HG U133A chip experiment process is as follows:

[0063] Step 1: Extraction of RNA.

[0064] According to the manufacturer's instructions, use QIAGEN's RNeasy Total RNA Isolation kit to extract total RNA from human breast cancer tissues and para-cancerous tissues; use QIAGEN's Oligotex Direct mRNA kit to extract mRNA from total RNA.

[0065] Step 2: RNA precipitation.

[0066] It is not necessary to precipitate total RNA after isolation or washing with QIAGEN’s RNeasy Total RNA Isolation kit. Adjust the elution volume to prepare cDNA synthesis close to the desired RNA concentration. ...

Embodiment 2

[0184] Embodiment 2. The present invention is illustrated by taking human liver cancer and normal tissue gene expression data GSE14520-GPL571 and GSE46408 obtained in the public database Gene Expression Ominbus as examples:

[0185]GSE14520-GPL571 contains gene expression data of 19 human liver cancer tissue samples and 19 corresponding non-tumor tissue samples. The IDs of the gene expression datasets are GSM362950, ​​GSM362951, GSM362952, GSM362953, GSM362954, GSM362955, GSM362956, GSM362957, GSM36343420, 2GSM1 、GSM363422、GSM363423、GSM363424、GSM363425、GSM363426、GSM363427、GSM363428、GSM363429、GSM363430、GSM363431、GSM363432、GSM363433、GSM363434、GSM363435、GSM363436、GSM363437、GSM363438、GSM363439、GSM363440、GSM363441、GSM363442、GSM363443、GSM363444、GSM363445、GSM363446 , GSM363447, GSM363448 and GSM363449, the chip platform used for gene expression detection is Affmetrix HG U133A 2.0. GSE46408 contains the gene expression data of 6 human liver cancer tissue samples and 6 corresponding no...

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Abstract

The invention belongs to the technical field of biological information. The invention provides a method for integrating gene expression data by crossing a plurality of different chip platforms; the method comprises the following steps: the standard preprocessing is implemented for the gene expression profile of the plurality of chip platforms; the common gene expression data in the different chip platforms is merged; genes are divided into k subsets according to the expression similarity of the genes on the plurality of chip platforms; the expression linear relation exps1=as*exps2+bs of the different chip platforms in every gene subset can be calculated by the least square method; the gene expression values of the different chip platforms are standardized into the same change range by using the formula exp1=X*A.*exp2+X*B to obtain standard gene expression matrixes, wherein the implications of symbols are defined as the specification.

Description

[0001] technical field [0002] The invention belongs to the technical field of biological information, in particular to the field of gene expression data analysis. Background technique [0003] At present, microarray chips have developed into a common high-throughput experimental technology for systematically studying biological problems, and there are different types of chip platforms and their manufacturers. Over the years, a large number of chip data sets have been accumulated, such as the GEO chip database of the National Center for Biotechnology Information NCBI and the ArrayExpress chip database of the European Bioinformatics Institute EBI. Among them, the NCBI GEO chip data has collected the data of about 1,008,760 samples and a total of 12,090 experiments, and the EBI ArrayExpress chip data has collected 43,124 experiments and a total of 1,223,250 microarray chip data. Due to the relatively expensive price of the chip experiment, the workload of sample collection a...

Claims

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Application Information

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IPC IPC(8): G06F19/24
Inventor 杭兴宜陈胜
Owner 艾吉泰康(嘉兴)生物科技有限公司
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