CN107133494A - A kind of new analysis biological genome copies the method for visualizing of number variation - Google Patents
A kind of new analysis biological genome copies the method for visualizing of number variation Download PDFInfo
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- CN107133494A CN107133494A CN201710266656.1A CN201710266656A CN107133494A CN 107133494 A CN107133494 A CN 107133494A CN 201710266656 A CN201710266656 A CN 201710266656A CN 107133494 A CN107133494 A CN 107133494A
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
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Abstract
The invention discloses the method for visualizing that a kind of new analysis biological genome copies number variation, all genes of each chromosome, abscissa is used as according to the ucstart positions of each gene, the average or median of the corresponding all sample copy numbers of the gene are used as the longitudinal axis, then scatterplot is drawn with MATLAB, a kind of color represents a kind of cancer.If contrasting kinds cancer type, we know it is which kind of cancer types according to what color can just will be apparent that, and the comparison effect of visualization between them is optimal.If contrasting the tumor sample and normal sample under same cancer types, tumor sample is expressed as a kind of color, and normal sample is expressed as another color, and the comparison effect of visualization between them is also optimal.Method for visualizing compared to before, our this method for visualizing, can be apparent from the copy number variation of the different cancer types of clear contrast or the copy number variation of different type sample is contrasted under same cancer types.
Description
Technical field
The invention belongs to bioinformatics or the technical field of gene technology, it is related to a kind of offer biological gene visual
Method.
Background technology
With the development of bioscience, after the completion of the Human Genome Project, exploration of the mankind to biological phenomena is more and more deeper
Enter.It is known that human body gene gene more than 30,000, they are made up of about 3,000,000,000 base-pairs, are distributed in nucleus
23 pairs of chromosomes in.
DNA sequence dna total amount is an astronomical figure really, but the function macro-molecular protein of researching DNA and its coding,
Day by day the sequence and structure increased is collected, arranged, stored, issues, extracts and processed.And therefrom analyze and find newly
Sequence, so as to constantly disclose the molecular basis of Human Physiology and pathologic process, is provided for the prevention of human diseases, diagnosis and treatment
Foundation, its meaning is very great, and has formd " bioinformatics " new branch of science.
Full-length genome copies the visual research of number variation, is also an important content.Current full-length genome copy number
The visualization method that makes a variation is relatively simple, is characterized in intuitive and convenient, but copy number variation is carried out under multiple cancer types
Contrast, or the effect of the contrast of the copy number variation of different type sample is not fine under same cancer types.
The content of the invention
In order to solve problems of the prior art, the present invention provides a kind of new analysis biological genome copy number and become
Different method for visualizing (Mountain plot), overcomes and copy number variation contrast is carried out under multiple cancer types in the prior art,
Or under same cancer types different type sample copy number variation contrast effect it is bad the problem of.
The technical scheme is that：A kind of new analysis biological genome copies the method for visualizing of number variation, including
Following steps：
(1) determination of transverse and longitudinal coordinate：Human body has 22 autosomes, and gene gene more than 30,000, each gene has
Which specific corresponding chromosome and corresponding specific original position, all genes of each chromosome (22 chromosomes,
Namely 22 figures), according to the original position of each gene as abscissa, with the mean value function in matlab softwares or in
Function of the location number travels through the corresponding all sample copy numbers of the gene, regard the average or I d median of the gene as ordinate；
(2) draw：With the plot functions in matlab, graphical pointv；Because the gene number on every chromosome is a lot, institute
It is that point is very close to have the result drawn out；
(3) there is specific position coordinates in the centromere of every chromosome in biology, with the line functions in matlab, uses
The perpendicular thick stick of black shows centromere, while by chromosome p arms, the gene on q arms is separated.
The beneficial effects of the invention are as follows：
Method for visualizing compared to before, our this method for visualizing, can be apparent from clear contrast several
The copy number variation of different cancer types copy number variation of different type sample either under same cancer types
Contrast.The black in centromere erects thick stick, and two arms of chromosome are separated.It is autosomal 22 with a kind of very intuitive way
The copy number state value of all genes is showed.
Brief description of the drawings
Fig. 1 is adenocarcinoma of lung, squamous cell lung carcinoma tumor sample and non-tumour tuberculosis sample copying in the range of full-length genome
Shellfish number variation distribution map；
Wherein red part represents the variation distribution of adenocarcinoma of lung tumour copy number, and blue portion represents lung squamous cancer tumour and copied
The variation distribution of shellfish number variation；Green portion represents the distribution of non-malignant tuberculosis sample copy number, and how many sample wherein n represents
Number.
Embodiment
The present invention will be described in detail with reference to the accompanying drawings and detailed description.
For a kind of cancer types, human body gene gene more than 30,000, each gene has which specific corresponding dye
Colour solid and corresponding specific original position ucstart, we are each chromosome (22 chromosomes, that is, 22 figures)
All genes, according to the ucstart positions of each gene as abscissa, the average of the corresponding all sample copy numbers of the gene
Or then median draws scatterplot, a kind of color represents a kind of cancer as the longitudinal axis with MATLAB plot functions.As above scheme
It is shown：The gene copy number state value of the sample of three types, can intuitively be contrasted very much.
Generally speaking, if to contrast kinds cancer type, we know which kind of is according to what color can just will be apparent that
Cancer types, the comparison effect of visualization between them is optimal.If contrast tumor sample under same cancer types and
Normal sample, tumor sample is expressed as a kind of color, and normal sample is expressed as another color, and the comparison between them is visual
It is also optimal to change effect.And we are labelled with the perpendicular thick stick of black according to the position in centromere, by chromosome p arms, on q arms
Gene is separated.This method for visualizing that we invent, carries out the contrast of copy number variation under multiple cancer types, or
The contrast of person's copy number variation of different type sample under same cancer types, both of these case can be done.
Described above is only the preferred embodiment of the present invention, it is noted that for the ordinary skill people of the art
For member, under the premise without departing from the principles of the invention, some improvements and modifications can also be made, these improvements and modifications also should
It is considered as protection scope of the present invention.
Claims (1)
1. a kind of new analysis biological genome copies the method for visualizing of number variation, it is characterised in that comprise the following steps：
(1) determination of transverse and longitudinal coordinate：Human body has 22 autosomes, and gene gene more than 30,000, each gene has specifically
Which corresponding chromosome and corresponding specific original position, all genes of each chromosome, according to each gene
Original position travels through the gene with the mean value function in matlab softwares or median function corresponding all as abscissa
Sample copy number, regard the average or I d median of the gene as ordinate；
(2) draw：With the plot functions in matlab, graphical pointv；Because the gene number on every chromosome is a lot, Suo Youhui
The result made is that point is very close；
(3) there is specific position coordinates in the centromere of every chromosome in biology, with the line functions in matlab, uses black
Perpendicular thick stick centromere is showed, while by chromosome p arms, the gene on q arms is separated.
Priority Applications (1)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| CN201710266656.1A CN107133494A (en) | 2017-04-21 | 2017-04-21 | A kind of new analysis biological genome copies the method for visualizing of number variation |
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| Application Number | Priority Date | Filing Date | Title |
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| CN201710266656.1A CN107133494A (en) | 2017-04-21 | 2017-04-21 | A kind of new analysis biological genome copies the method for visualizing of number variation |
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| CN107133494A true CN107133494A (en) | 2017-09-05 |
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| Application Number | Title | Priority Date | Filing Date |
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| CN201710266656.1A Pending CN107133494A (en) | 2017-04-21 | 2017-04-21 | A kind of new analysis biological genome copies the method for visualizing of number variation |
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Cited By (1)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110021363A (en) * | 2017-12-25 | 2019-07-16 | 安诺优达基因科技(北京)有限公司 | For constructing the device and method of user friendly chromosomal gene variation map |
-
2017
- 2017-04-21 CN CN201710266656.1A patent/CN107133494A/en active Pending
Non-Patent Citations (3)
| Title |
|---|
| ANA H.BARRAGÁN LID: ""Profiling of DNA copy number in sarcomas by array comparative genomic hybridization and identification of candidate cancer genes"", 《UNIVERSITY OF OSLO》 * |
| DARREN A ABBEY等: ""YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens"", 《GENOME MEDICINE》 * |
| ZHE-WEI QIU等: ""Genome-wide copy number variation pattern analysis and a classification signature for non-small cell lung cancer"", 《HTTPS://DOI.ORG/10.1002/GCC.22460》 * |
Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN110021363A (en) * | 2017-12-25 | 2019-07-16 | 安诺优达基因科技(北京)有限公司 | For constructing the device and method of user friendly chromosomal gene variation map |
| CN110021363B (en) * | 2017-12-25 | 2021-01-15 | 安诺优达（义乌）医学检验有限公司 | Device and method for constructing user-friendly chromosome gene variation map |
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Application publication date: 20170905 |