CN105243293B - The collection of prostate Related oncogene information and analysis system and method - Google Patents
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Abstract
The present invention relates to the collection of prostate Related oncogene information and analysis methods.Invention provides a kind of prostate Related oncogene information and collects and analysis system, it is collected by the data to prostate cancer related in existing database, confluence analysis is carried out using mRNA and miRNA high throughput transcript profile data of the bioinformatics method to the prostate cancer of collection, handles to obtain the prostate cancer diagnosis marker suitable for clinical application based on large sample big data.
Description
Technical field
The present invention relates to B ioinformation data management fields, and in particular to prostate Related oncogene information is collected and analysis
Method.
Background technique
Prostate cancer (prostate cancer) is common male genitourinary tract infections tumour.So far, prostate cancer
The mechanism of occurrence and development is unclear.High-throughput techniques provide for the research of disease pathogenesis more divides comprehensively and quickly
Analysis means, therefore a large amount of scholars utilize genetic chip or high throughput sequencing technologies to mRNA the and miRNA transcript profile of prostate cancer
It is studied, still, each researcher or laboratory are due to limited material or the limited sequencing for being only capable of completing small sample of funds
Analysis, but in the pathogenic process of cancer, cancer cell obtains the accumulation of survival advantage, constantly expands, and produces to surrounding tissue environment
Raw infiltration, the process spread need the genetic structure of series of genes to change, and need to the research of these variations
The processing of large sample big data could be obtained more accurately.
The present invention is collected by the data to prostate cancer related in existing database, utilizes bioinformatics
Method carries out confluence analysis to mRNA the and miRNA high throughput transcript profile data of the prostate cancer of collection, thus to prostate cancer
Pathogenesis probed into, certain Research foundation is provided for its diagnosing and treating.Exploitation for later period drug target provides
With reference to.
Summary of the invention
The purpose of the present invention is to provide a kind of collection of prostate Related oncogene information and analysis systems, including data to adopt
Collect module, data analysis module and data disaply moudle, data acquisition module sends data analysis module to after collecting data, number
It is shown to after data progress Machining Analysis by data disaply moudle according to analysis module, the data acquisition module includes DNA number
According to acquisition module, RNA data acquisition module and protein data acquisition module.
Further, the DNA data are genomic data, and the RNA data are transcript profile data, and the protein data is
Proteomic data.Data are high-flux sequence data, including chip sequencing and the sequencing of two generations.
Further, the DNA data acquisition module includes mutational site acquisition module, methylation sites acquisition module, SNP
Site acquisition module；The RNA data acquisition module include mRNA expression acquisition module, miRNA expression acquisition module,
LncRNA expresses acquisition module；Protein data acquisition module includes protein expression profiling data acquisition module.
The mutation includes the missing of point mutation caused by single sequence change or multiple bases, repeats and be inserted into.
Further, the data analysis module includes difference expression gene analysis module, prediction target spot analysis module, biology
Information Network analysis module, GO analysis module, pathway analysis module.
Further, biological information net analysis include differential expression miRNA and target gene establish biological information network,
The biological information network between biological information network, gene and albumen between gene and gene.
Further, the prediction target spot analysis and utilization includes DIANAmT, miRanda, miRDB, miRWalk, PICTAR5
And the target spot of these algorithm forecasted variances of Targetscan expression miRNA, preferably >=4 algorithm predict the target spot come.
Further, downloaded from existing database the relevant mutational site data of prostate cancer, methylation sites data,
SNP site data, mRNA expression data, miRNA expression data, lncRNA express data, protein expression profiling data.
Further, data acquisition module downloads sequencing data from GEO database, SRA database, ICGC database.
Further, the prostate Related oncogene information is collected and analysis system further includes data preprocessing module, number
Data analysis mould is sent to by data preprocessing module progress background correction and after standardizing after collecting data according to acquisition module
Block.
The purpose of the present invention is to provide a kind of collection of prostate Related oncogene information and analysis methods, comprising:
(1) prostate cancer sample sequencing initial data is downloaded from existing database and initial data is sequenced in check sample；
(2) background correction and standardization are carried out to the initial data of downloading；
(3) data are analyzed；
(4) display analysis result.
Further, the analysis of difference expression gene prediction target spot, the analysis of biological information net, GO points are carried out to data
Analysis, pathway analysis.
Further, biological information net analysis include differential expression miRNA and target gene establish biological information network,
The biological information network between biological information network, gene and albumen between gene and gene.
Further, the prediction target spot analysis and utilization includes DIANAmT, miRanda, miRDB, miRWalk, PICTAR5
And the target spot of these algorithm forecasted variances of Targetscan expression miRNA, preferably >=4 algorithm predict the target spot come.
It is preferred that carrying out the analysis of transcript profile data using R software.
Further, downloaded from existing database the relevant mutational site data of prostate cancer, methylation sites data,
SNP site data, mRNA expression data, miRNA expression data, lncRNA express data, protein expression profiling data.
Further, sequencing data is downloaded from GEO database, SRA database, ICGC database.
The purpose of the present invention is to provide one group of prostate cancer diagnosis and treatment markers, including miRNA:hsa-miR-183, hsa-
miR-153、hsa-miR-96、hsa-miR-25、hsa-miR-93、hsa-miR-182、hsa-miR-663、 hsa-miR-
106b,hsa-miR-130b,hsa-miR-18a；And/or mRNA:SIM2, HPN, AMACR, MYC, OR51E2, BICD1,
DNAH5、PCA3、ARHGEF38、TRIB1、REPS2、GJB1、 EPCAM、PCSK6、CAMKK2、STIL、SLC12A8、
GNPNAT1,PVT1,TMTC4；The up-regulation of said gene is positively correlated with prostate cancer risk is suffered from.
The purpose of the present invention is to provide one group of prostate cancer markers, including miRNA:hsa-miR-222, hsa-
miR-224、hsa-miR-99b、hsa-miR-221、hsa-miR-204、hsa-miR-181c、hsa-miR-378、 hsa-
miR-452、hsa-miR-378、hsa-miR-31、hsa-miR-139-5p、hsa-miR-505、 hsa-miR-133a、hsa-
miR-328,hsa-miR-27b,hsa-miR-154,hsa-miR-324-5p, hsa-miR-487b,hsa-miR-502-5p；
And/or mRNA:TCEAL2, CPA6, C15orf41, VSNL1, KANK1, NYNRIN, NAV2, ZNF185, STARD5, GSTP1,
ROR2,DUOX1,ALAD, ST5,DBNDD2,SEMA6D,BCL2,DOK4,ST6GALNAC2,ACACB；The downward of said gene
It is positively correlated with prostate cancer risk is suffered from.
Detailed description of the invention
Fig. 1 prostate Related oncogene information collects and surveys system schematic
Fig. 2 prostate Related oncogene information data collection module map
Fig. 3 prostate Related oncogene information data analysis module figure
Fig. 4 prostate Related oncogene information collects and surveys system diagram
Fig. 5 prostate Related oncogene information collects and surveys system detail drawing
Specific embodiment
Present invention will be further explained below with reference to specific examples, for explaining only the invention, and should not be understood as to this
The limitation of invention.It will be understood by those skilled in the art that: without departing from the principle and spirit of the present invention may be used
To carry out a variety of change, modification, replacement and modification to these embodiments, the scope of the present invention is limited by claim and its equivalent
It is fixed.In the following examples, the experimental methods for specific conditions are not specified, usually according to normal condition or according to item proposed by manufacturer
Part examinations.
Embodiment 1
A kind of prostate Related oncogene information collection and analysis system (see Fig. 1), including the analysis of data acquisition module, data
Module and data disaply moudle, data acquisition module send data analysis module, data analysis module logarithm to after collecting data
It is shown according to after progress Machining Analysis by data disaply moudle, wherein data acquisition module includes DNA data acquisition module, RNA
Data acquisition module and protein data acquisition module.
Embodiment 2
A kind of data collection module (see Fig. 2) in prostate Related oncogene information collection and analysis system, including DNA
Data acquisition module, RNA data acquisition module and protein data acquisition module, wherein DNA data acquisition module includes mutation position
Point acquisition module, methylation sites acquisition module, SNP site acquisition module；RNA data acquisition module includes that mRNA expression is adopted
Collect module, miRNA expression acquisition module, lncRNA and expresses acquisition module；Protein data acquisition module includes protein expression profiles number
According to acquisition module.
Embodiment 3
A kind of data analysis module (see Fig. 3) in prostate Related oncogene information collection and analysis system, including difference
Different expressing gene analysis module, prediction target spot analysis module, biological information net analysis module, GO analysis module, pathway analysis
Module.
Embodiment 4
A kind of prostate Related oncogene information collection and analysis system (see Fig. 4), including data acquisition module, data are located in advance
Manage module, data analysis module and data disaply moudle, data acquisition module collect after data by data preprocessing module into
Send data analysis module after row background correction and standardization to, data analysis module passes through number after carrying out Machining Analysis to data
It is shown according to display module, wherein data acquisition module includes DNA data acquisition module, RNA data acquisition module and protein data
Acquisition module.
Embodiment 5
A kind of prostate Related oncogene information collection and analysis system (see Fig. 5), including data acquisition module, data are located in advance
Manage module, data analysis module and data disaply moudle, data acquisition module collect after data by data preprocessing module into
Send data analysis module after row background correction and standardization to, data analysis module passes through number after carrying out Machining Analysis to data
It is shown according to display module, wherein data acquisition module includes DNA data acquisition module, RNA data acquisition module and protein data
Acquisition module.Wherein, DNA data acquisition module includes mutational site acquisition module, methylation sites acquisition module, SNP site
Acquisition module；RNA data acquisition module includes mRNA expression acquisition module, miRNA expression acquisition module, lncRNA expression acquisition
Module；Protein data acquisition module includes protein expression profiling data acquisition module.Data analysis module includes difference expression gene
Analysis module, prediction target spot analysis module, biological information net analysis module, GO analysis module, pathway analysis module.
The collection of 6 data of embodiment
Part prostate cancer data in GEO database are collected, specific data are shown in Table 1.
The basic condition of 1.3 sets of prostate cancer high throughput mRNA and miRNA data sets of table
The processing of 7 data of embodiment
After carrying out background correction and standardization to 3 sets of miRNA and mRNA initial data by transcript profile Data Analysis Software
It carries out t-test and obtains P value, calculate effect quantity, then examined using Fisher and merge P value, merged using random-effect model and imitated
Ying Liang screens differential expression miRNA and mRNA, sets P value < 0.01, effect quantity > 0.8, filters out 29 miRNA altogether, wherein
Gene 10 of expression up-regulation, gene 19 of expression downward.As shown in table 2, wherein left side is expression up-regulation
MiRNA, right side are the miRNA that expression is lowered.P value < 0.01 is set in analytic process, effect quantity > 1 filters out 946 altogether
MRNA, wherein gene 17 7 of expression up-regulation, enumerate its up-regulation or lower ranking by gene 769 of expression downward
Preceding 20 mRNA (being shown in Table 3).
The significant miRNA raised and lower of 2. prostate cancer of table expression
Significant (preceding 20) mRNA raised and lower of 3. prostate cancer of table expression
The identification of the miRNA target gene of 8 prostate cancer differential expression of embodiment
Identification miRNA target gene is the extremely important step for studying specific organization and cell miRNA function.Using including
These algorithm forecasted variances of DIANAmT, miRanda, miRDB, miRWalk, PICTAR5 and Targetscan express miRNA's
Target gene chooses the differential expression that >=4 algorithms predict the target gene come, and have verified that in miRWalk database lookup
Then gene negatively correlated with miRNA expression in all target genes and mRNA chip is carried out integration point by the target gene of miRNA
Analysis, 751 target genes are obtained in we, obtain the target gene of 574 up-regulation miRNA, 128 downward miRNA by predicting
Target gene, and by miRWalk database obtain 24 have verified that expression up-regulation miRNA target genes, 35 are
The target gene for the miRNA that the expression of verifying is lowered.
The biological information network of the target gene of 9 prostate cancer differential expression miRNA of embodiment and differential expression composition
It is made of using Cytoscape software building the target gene of prostate cancer differential expression miRNA and differential expression
Biological information network.The miRNAs and mRNAs shown in figure differential expression in prostate cancer.If central point is on significant
The miRNAs of tune, that around central point is the mRNAs significantly lowered, if central point is the miRNAs significantly lowered, surrounds center
Point is the mRNAs significantly raised.
The functional annotation of the target gene of 10 prostate cancer differential expression of embodiment
In order to preferably study the function of differential expression target gene, we are carried out by gene of the DAVID to differential expression
The enrichment of GO function and the enrichment of KEGG access, the GO function and KEGG access of preceding 15 significant enrichments are shown in Table 4 and table 5.KEGG access
The target gene of 188 differential expressions as the result is shown of enrichment can sift out in the library KEGG, concentrate on cancer access, talin,
Melanogenesis, glutamatergic synaptic, Wnt signal path, Small Cell Lung Cancer, purine metabolism, axon guidance, pentose phosphate pathway,
30 signal paths such as actin cytoskeleton adjusting.
The GO function of 4. preceding 15 differential expression target gene significant enrichments of table
The signal path of 5. preceding 15 differential expression target gene significant enrichments of table
Claims (8)
1. a kind of prostate Related oncogene information is collected and analysis system, including data acquisition module, data analysis module and
Data disaply moudle, data acquisition module send data analysis module to after collecting data, and data analysis module carries out data
It is shown after Machining Analysis by data disaply moudle, the data acquisition module includes that DNA data acquisition module, RNA data are adopted
Collect module and protein data acquisition module, the data analysis module include difference expression gene analysis module, which is characterized in that
Difference expression gene analysis module analyzes difference expression gene, and difference expression gene is following miRNA:hsa-miR-183, hsa-
miR-153、hsa-miR-96、hsa-miR-25、hsa-miR-93、hsa-miR-182、hsa-miR-663、hsa-miR-
106b,hsa-miR-130b,hsa-miR-18a；And/or mRNA:SIM2, HPN, AMACR, MYC, OR51E2, BICD1,
DNAH5、PCA3、ARHGEF38、TRIB1、REPS2、GJB1、EPCAM、PCSK6、CAMKK2、STIL、SLC12A8、GNPNAT1、
PVT1,TMTC4；Or difference expression gene is following miRNA:hsa-miR-222, hsa-miR-224, hsa-miR-99b, hsa-
miR-221、hsa-miR-204、hsa-miR-181c、hsa-miR-378、hsa-miR-452、hsa-miR-378、hsa-miR-
31、hsa-miR-139-5p、hsa-miR-505、hsa-miR-133a、hsa-miR-328、hsa-miR-27b、hsa-miR-
154,hsa-miR-324-5p,hsa-miR-487b,hsa-miR-502-5p；And/or mRNA:TCEAL2, CPA6,
C15orf41、VSNL1、KANK1、NYNRIN、NAV2、ZNF185、STARD5、GSTP1、ROR2、DUOX1、ALAD、ST5、
DBNDD2、SEMA6D、BCL2、DOK4、ST6GALNAC2、ACACB。
2. system according to claim 1, which is characterized in that the DNA data acquisition module includes mutational site acquisition
Module, methylation sites acquisition module, SNP site acquisition module；The RNA data acquisition module includes mRNA expression acquisition mould
Block, miRNA expression acquisition module, lncRNA express acquisition module；Protein data acquisition module includes that protein expression profiling data is adopted
Collect module.
3. system according to claim 1, which is characterized in that the data analysis module further includes prediction target spot analysis mould
Block, biological information net analysis module, GO analysis module, pathway analysis module.
4. system according to claim 1, which is characterized in that the prostate Related oncogene information is collected and analysis system
System further includes data preprocessing module, data acquisition module collect after data by data preprocessing module carry out background correction with
Send data analysis module after standardization to.
5. a kind of prostate Related oncogene information is collected and analysis method, comprising:
(1) prostate cancer sample sequencing initial data is downloaded from existing database and initial data is sequenced in check sample；
(2) background correction and standardization are carried out to the initial data of downloading；
(3) data are analyzed；
(4) display analysis result；
It is characterized in that, carrying out analysis to data includes carrying out difference expression gene analysis to data, under difference expression gene is
Arrange miRNA:hsa-miR-183, hsa-miR-153, hsa-miR-96, hsa-miR-25, hsa-miR-93, hsa-miR-182,
hsa-miR-663,hsa-miR-106b,hsa-miR-130b,hsa-miR-18a；And/or mRNA:SIM2, HPN, AMACR,
MYC、OR51E2、BICD1、DNAH5、PCA3、ARHGEF38、TRIB1、REPS2、GJB1、EPCAM、PCSK6、CAMKK2、
STIL,SLC12A8,GNPNAT1,PVT1,TMTC4；Or difference expression gene is following miRNA:hsa-miR-222, hsa-
miR-224、hsa-miR-99b、hsa-miR-221、hsa-miR-204、hsa-miR-181c、hsa-miR-378、hsa-miR-
452、hsa-miR-378、hsa-miR-31、hsa-miR-139-5p、hsa-miR-505、hsa-miR-133a、hsa-miR-
328,hsa-miR-27b,hsa-miR-154,hsa-miR-324-5p,hsa-miR-487b,hsa-miR-502-5p；And/or
MRNA:TCEAL2, CPA6, C15orf41, VSNL1, KANK1, NYNRIN, NAV2, ZNF185, STARD5, GSTP1, ROR2,
DUOX1、ALAD、ST5、DBNDD2、SEMA6D、BCL2、DOK4、ST6GALNAC2、ACACB。
6. according to the method described in claim 5, it is characterized in that, carrying out difference expression gene prediction target spot to data
Analysis, the analysis of biological information net, GO analysis, pathway analysis.
7. according to the method described in claim 6, it is characterized in that, biological information net analysis includes differential expression miRNA
Biology between target gene biological information network, the biological information network between gene and gene, gene and the albumen established
Information network；The prediction target spot analysis and utilization includes DIANAmT, miRanda, miRDB, miRWalk, PICTAR5 and
The target spot of these algorithm forecasted variances of Targetscan expression miRNA.
8. according to the method described in claim 5, it is characterized in that, downloading the relevant mutation of prostate cancer from existing database
Site data, methylation sites data, SNP site data, mRNA expression data, miRNA expression data, lncRNA express number
According to, protein expression profiling data.
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| CN106709275A (en) * | 2017-02-04 | 2017-05-24 | 上海喆之信息科技有限公司 | Restricted type cardiomyopathy gene data processing device |
| CN107227342A (en) * | 2017-05-04 | 2017-10-03 | 上海大学 | Prostate cancer diagnosis genome and its application |
| CN107630092B (en) * | 2017-10-23 | 2020-03-31 | 广州医科大学附属第二医院 | Application of miR-505-3p in diagnosis, prognosis and treatment of bone metastasis of prostate cancer |
| CN108319818B (en) * | 2018-02-07 | 2018-12-07 | 中国科学院生物物理研究所 | A kind of method of the SNP site of predicted impact long non-coding RNA biological function |
| CN114333992A (en) * | 2020-09-30 | 2022-04-12 | 北京瑷格干细胞科技有限公司 | System and method for collecting and analyzing skin aging related gene information |
| CN114628022A (en) * | 2020-12-14 | 2022-06-14 | 北京致成生物医学科技有限公司 | Osteoporosis related gene screening and function analysis method and system |
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