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Identification method of individual differential expression protein

A technology of differential expression and identification method, which is applied in proteomics, instrumentation, genomics, etc., can solve problems such as performance improvement, and achieve the effect of ensuring stability, good application prospects, and high recognition accuracy

Pending Publication Date: 2022-03-22
XIAMEN UNIV
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

However, due to the differences between protein data and miRNA, IncRNA data
The performance of these methods on protein data still needs to be improved

Method used

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  • Identification method of individual differential expression protein
  • Identification method of individual differential expression protein
  • Identification method of individual differential expression protein

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Experimental program
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Embodiment

[0042] Such as Figure 1 to Figure 4 As shown, the present invention discloses a method for identifying individual differentially expressed proteins, the method comprising the following steps:

[0043] S1. Preprocessing the protein abundance data;

[0044] The specific process of step S1 is:

[0045] S11. Perform statistics on the ratio of missing values ​​for each protein in all samples in the protein abundance data, filter proteins by setting the upper limit of the missing value ratio, and remove proteins whose missing value ratio exceeds the threshold in the protein abundance data;

[0046]S12. By calculating the coefficient of variation of proteins in the same cohort, it is judged whether the difference in protein abundance among different individuals is due to heterogeneity among individuals or quantitative errors;

[0047] Proteins with a high coefficient of variation in the same cohort in step S12 are identified as caused by quantitative errors, and are screened out; ...

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Abstract

The invention discloses a method for identifying individual differential expression proteins. The method comprises the following steps: S1, preprocessing protein abundance data; s2, verifying whether highly significant protein pairs exist in the protein abundance data of the normal queue; s3, selecting a reference group in an individual level differential expression algorithm; s4, identifying differential expression proteins by adopting an individual level differential expression algorithm based on the reference group; the method comprises the following steps: firstly, based on the characteristics of protein abundance data, preprocessing the protein abundance data, removing proteins with high variation coefficients and high missing value proportions, and reducing the influence of protein quantitative errors on individual differential protein results; and secondly, a reference group is selected based on the protein stability pair, and proteins with differential expression in the reference group are continuously optimized by using an iteration method, so that the stability of the reference group is ensured, the proteins with differential expression can be effectively identified on the individual level, the identification precision is high, and the application prospect is good.

Description

technical field [0001] The invention relates to the field of biotechnology, in particular to a method for identifying individual differentially expressed proteins. Background technique [0002] The Clinical Proteomics Tumor Analysis Consortium (CPTAC) developed a standard workflow for LC-MS-based proteomics measurements in human tumor tissues and applied this workflow to colorectal, ovarian, and Breast Cancer Data (TCGA). Following this initial study, the proteomics of 13 other cancer types were also comprehensively characterized. These CPTAC studies explored trans-acting genomic aberrations in protein expression, reclassified molecular subtypes based on proteomics, and identified pathways using phosphoproteomics. Since most CPTAC studies did not analyze normal tissues, the accuracy of differential expression analysis results could not be assessed. Sample heterogeneity further complicates proteomic analysis and limits the ability to analyze individual altered cancer prote...

Claims

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Application Information

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IPC IPC(8): G16B25/10G16B20/20G16B40/00
CPCG16B25/10G16B20/20G16B40/00
Inventor 俞容山刘亚琛童梦莎林雅岚吴雨娟林育祥
Owner XIAMEN UNIV
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