data_analysis

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data_analysis [2019/07/06 02:36]
tongyifan created
data_analysis [2019/07/06 02:41]
tongyifan
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 ====== Data Analysis ====== ====== Data Analysis ======
  
 Note: Note:
  
-→ Until now, all data was downloaded from the "​Legacy GDC portal"​ which was updated before 10/05/2016. New updated data is coming! +  * Until now, all data was downloaded from the "​Legacy GDC portal"​ which was updated before 10/05/2016. New updated data is coming! 
- +  ​* ​Gene expression is the level 3 data preprocessed by TCGA which was measured by the platform Illumina HiSeq 2000 RNA Sequencing Version 2. 
-→ Gene expression is the level 3 data preprocessed by TCGA which was measured by the platform Illumina HiSeq 2000 RNA Sequencing Version 2. +  ​* ​The level 3 CNV (Copy Number Variation) data was measured by Affymetrix Genome-Wide Human SNP Array 6.0.
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-→ The level 3 CNV (Copy Number Variation) data was measured by Affymetrix Genome-Wide Human SNP Array 6.0.+
  
 Please go to [[https://​portal.gdc.cancer.gov/​legacy-archive/​search/​f|Legacy GDC portal]] and Data Preprocessing section for more details of these data. More category data GWAS analyzing methods are coming! Please go to [[https://​portal.gdc.cancer.gov/​legacy-archive/​search/​f|Legacy GDC portal]] and Data Preprocessing section for more details of these data. More category data GWAS analyzing methods are coming!
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 There are several areas in this page including: There are several areas in this page including:
  
-♦  ​Overview area: an overview of cancer types whose data are available +  * Overview area: an overview of cancer types whose data are available 
- +  ​Brief step by step guide: Brief demonstration of how to start to use the analyses provided by us 
-♦  Brief step by step guide: Brief demonstration of how to start to use the analyses provided by us +  ​Data plots area: Examples and brief descriptions of data plotting methods 
- +  ​Data mining area: Examples and brief descriptions of data mining methods 
-♦  Data plots area: Examples and brief descriptions of data plotting methods +  ​Link area: Links that might be helpful to you
- +
-♦  Data mining area: Examples and brief descriptions of data mining methods +
- +
-♦  Link area: Links that might be helpful to you+
  
 ===== Overview area ===== ===== Overview area =====
  
-{{http://​www.clickgenome.org/​img/​guide/​7.png?​nolink&​80%}}+{{http://​www.clickgenome.org/​img/​guide/​7.png?​nolink&​904x499}}
  
-1、Navigation bar: You can switch to any other pages through the links provided here. +  - Navigation bar: You can switch to any other pages through the links provided here. 
- +  ​- ​Speed buttons: You can click “How to Start” button to skip to the Brief demonstration area in this page to know how to get it started. You also can click “Go to Analyze” button to skip to the to Data Plots area to select the analyze function you want to use. 
-2、Speed buttons: You can click “How to Start” button to skip to the Brief demonstration area in this page to know how to get it started. You also can click “Go to Analyze” button to skip to the to Data Plots area to select the analyze function you want to use. +  ​- ​Overview area: This is an overview histogram of how many cases in different cancer types are available for the analyze. 
- +  ​- ​We are devoted in helping with the oncogenetic research for free. But we need finical support to afford an advanced internet server who can provide big size data global transfer with a fantastic fast speed. Therefore, we are very appreciated for any donations.
-3、Overview area: This is an overview histogram of how many cases in different cancer types are available for the analyze. +
- +
-4、We are devoted in helping with the oncogenetic research for free. But we need finical support to afford an advanced internet server who can provide big size data global transfer with a fantastic fast speed. Therefore, we are very appreciated for any donations.+
  
 ===== Brief step by step guide ===== ===== Brief step by step guide =====
  
-{{http://​www.clickgenome.org/​img/​guide/​8.png?​nolink&​80%}} +{{http://​www.clickgenome.org/​img/​guide/​8.png?​nolink&​874x285}}
- +
-1) SIGN UP: To start using the analyze methods provided by us, you need to register and login first. Only email address is required for registration. For the same one email address, only one account is allowed. +
- +
-2) CHOOSE A METHOD: It's a list of all methods provided by us. You can click any of them to skip to the corresponding section of it directly.+
  
-3) ENJOY DATA ANALYSIS: After registering ,logging in and selecting a method, now you can enjoy available GWAS analyses.+  - SIGN UP: To start using the analyze methods provided by us, you need to register and login first. Only email address is required for registration. For the same one email address, only one account is allowed. 
 +  - CHOOSE A METHOD: It's a list of all methods provided by us. You can click any of them to skip to the corresponding section of it directly. 
 +  - ENJOY DATA ANALYSIS: After registering ,logging in and selecting a method, now you can enjoy available GWAS analyses.
  
 There are two kinds of GWAS methods provided by us: Data visualization and Data mining. There are two kinds of GWAS methods provided by us: Data visualization and Data mining.
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 The Beeswarm plot is a one-dimensional scatter plot like "​stripchart",​ but with closely-packed,​ non-overlapping points. Here, the Beeswarm plots with or without box plot are provided. It’s very helpful to see the distributions of certain genes in different ways. Therefore, we provide two kinds of Beeswarm plots: The Beeswarm plot is a one-dimensional scatter plot like "​stripchart",​ but with closely-packed,​ non-overlapping points. Here, the Beeswarm plots with or without box plot are provided. It’s very helpful to see the distributions of certain genes in different ways. Therefore, we provide two kinds of Beeswarm plots:
  
-Δ "​Bee-swarm plot_By Gene": Bee-swarms for given genes of samples across different cancer types are plotted in the same figure to compare their distributions fairly and easily. +  * "​Bee-swarm plot_By Gene": Bee-swarms for given genes of samples across different cancer types are plotted in the same figure to compare their distributions fairly and easily. 
- +  ​* ​"​Bee-swarm ​plot_By ​Cancer":​ Bee-swarms for different genes in samples of the same given cancer type are created in the same figure to compare their distributions fairly and easily.
-Δ "​Bee-swarm ​plot _ By Cancer":​ Bee-swarms for different genes in samples of the same given cancer type are created in the same figure to compare their distributions fairly and easily.+
  
 You can click the corresponding URLs right below the description and the examples of Bee-swarm plot to get into '​Bee-swarm plot_By Gene' or '​Bee-swarm plot _ By Cancer'​ page to create corresponding bee-swarms by yourself. You can click the corresponding URLs right below the description and the examples of Bee-swarm plot to get into '​Bee-swarm plot_By Gene' or '​Bee-swarm plot _ By Cancer'​ page to create corresponding bee-swarms by yourself.
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 //Note: up to now, only mRNA expression values and copy number variations of genes in TCGA/GDC data are available for Bee-swarm plot.// //Note: up to now, only mRNA expression values and copy number variations of genes in TCGA/GDC data are available for Bee-swarm plot.//
  
-{{http://​www.clickgenome.org/​img/​guide/​9.png?​nolink&​80%}}+{{http://​www.clickgenome.org/​img/​guide/​9.png?​nolink&​872x297}}
  
 ==== 2) Mountain plot ==== ==== 2) Mountain plot ====
  
-{{http://​www.clickgenome.org/​img/​guide/​10.png?​nolink&​80%}}+{{http://​www.clickgenome.org/​img/​guide/​10.png?​nolink&​872x254}}
  
 Mountain plot is named by Dr. Kai Song because its ups and downs look like mountains outlines seen from afar. It is a very useful scatter plot, created by Dr. Adi Gazdar and Dr. Kai Song, for visualizing and analyzing genome-wide variations of copy numbers [1, 2]. In Mountain plot, each spot is the median/mean value of copy numbers of each gene in a group which can be a batch or a cancer type. The genes are sorted according to their locations. The space between two arms of each chromosome is the location of the corresponding centromere. Mountain plot is named by Dr. Kai Song because its ups and downs look like mountains outlines seen from afar. It is a very useful scatter plot, created by Dr. Adi Gazdar and Dr. Kai Song, for visualizing and analyzing genome-wide variations of copy numbers [1, 2]. In Mountain plot, each spot is the median/mean value of copy numbers of each gene in a group which can be a batch or a cancer type. The genes are sorted according to their locations. The space between two arms of each chromosome is the location of the corresponding centromere.
  
-//Note: theoretically,​ Mountain plot can be used to visualizing mRNA expression values or methylation values of chromosomes.//​ ===== Link area =====+//Note: theoretically,​ Mountain plot can be used to visualizing mRNA expression values or methylation values of chromosomes.//​ 
 + 
 +===== Link area =====
  
 Necessary links are available for you to switch to other pages or websites. Necessary links are available for you to switch to other pages or websites.
  
-{{http://​www.clickgenome.org/​img/​guide/​11.png?​nolink&​80%}}+{{http://​www.clickgenome.org/​img/​guide/​11.png?​nolink&​868x131}}
  
  
  • data_analysis.txt
  • Last modified: 2019/07/06 02:41
  • by tongyifan