starBase v2.0 tutorialstarbase.sysu.edu.cn/starbase2/downloads/starBase_v2.0_tutorial.pdf ·...
Transcript of starBase v2.0 tutorialstarbase.sysu.edu.cn/starbase2/downloads/starBase_v2.0_tutorial.pdf ·...
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starBase v2.0 Tutorial
© 2010-2013, Jianhua Yang at Sun Yat-sen University
For comments, suggestions on the starBase platform, please contact us: [email protected]
On commercial use, contact: [email protected]
Cover Pan-Cancer Analysis
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Homepage
The distinctive features and improvements starBase v2.0
What starBase v2.0 includes
Link to starBase v1.0
Download the tutorial of starBase v2.0
TestimonialsHow to cite starBase
Examples
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Pan-Cancer miRNA-lncRNA
Select Number of Cancer Types
Note:Number of Cancer Types(Pan-Cancer) can be used to explore anti-correlation (pearson correlation: r<0, p-value<0.05) between miRNA and target genes across diverse cancer types. For example, cancer type >=1 means that expression of miRNA and target gene is anti-correlation (pearson correlation: r<0, p-value<0.05) at least one cancer type.
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Query Results: Pan-Cancer miRNA-lncRNA
Click miRNA to get detail and Pan-Cancer Expression Profiles
Click lncRNA to get detail and Pan-Cancer Expression Profiles
Click cancer Number to get detail and Pan-Cancer Expression Profiles for miRNA-lncRNA interactions
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① Pan-Cancer miRNA expression profiles
Query Results: Pan-Cancer miRNA-lncRNA
Select Pan-Cancer or single Cancer TypePrint or export figure
Expression Mean Value (log2) of normal samples
Fold-Change of Cancer/Normal samples
Mean Value (log2) of cancer samples
Cancer Types
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① Box-Plot miRNA expression profiles
Query Results: Pan-Cancer miRNA-lncRNA
Select single Cancer TypePrint or export figure
Normal samples
Cancer samples
sample information
Click Case Id to get clinical information
Fold-Change and t test p-value
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① Box-Plot lncRNA expression profiles
Query Results: Pan-Cancer miRNA-lncRNA
Select single Cancer TypePrint or export figure
Normal samples
Cancer samples
sample information
Click Case Id to get clinical information
Fold-Change and t test p-value
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① Pan-Cancer miRNA-lncRNA interactions
Query Results: Pan-Cancer miRNA-lncRNA
Cancer Types Sample Number r, p-value and False discovery rate (FDR)of pearson correlation analysis
click here
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① Pan-Cancer miRNA-lncRNA interactions
Query Results: Pan-Cancer miRNA-lncRNA
r value and p-value of pearson correlation analysis
click here
Select single Cancer TypeSelect Chart Type
Print or export figure
sample information
Click Case Id to get clinical information
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miRNA-lncRNA
① miRNA-lncRNA interactions.
The target information page
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miRNA-ncRNA
② miRNA-circRNA interactions.
The query page
The results and target information page are omitted because the interfaces are similar to the ones of miRNA-lncRNA interactions
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miRNA-ncRNA
③ miRNA-pseudogene interactions.
The query page
The results and target information page are omitted because the interfaces are similar to the ones of miRNA-lncRNA interactions
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miRNA-ncRNA
④ miRNA-sncRNA interactions.
The query page
The results and target information page are omitted because the interfaces are similar to the ones of miRNA-lncRNA interactions
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miRNA-mRNA
① miRNA-target intersections.
The query page
The 4th option is restrained by the 5th one. If the count of programs selected in the 5th option is more than the program number chose in the 4th
option, the 4th option is disable.
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miRNA-mRNA
Non-zero numbers are highlighted. Click on them for more details.
① miRNA-target intersections.
The results page
Export all query results as excel format
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miRNA-mRNA
① miRNA-target intersections.
The target information page
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miRNA-mRNA
Choose the interested clade, genome and assembly
Select a microRNA and a gene symbol
② miRNA-mRNA interactions.
The query page
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miRNA-mRNA
② miRNA-mRNA interactions.
The results page
Non-zero numbers are highlighted. Click on them for more details.
Export all query results as excel format
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miRNA-mRNA
② miRNA-mRNA interactions.
The target information page
Display the location in the deepView genome browser
Link to experiments sources information
Link to NCBI nucleotide database
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ceRNA Network
The query page
The minimum number of shared miRNAs of typed gene and its predicted ceRNAs
Type the gene symbol for its ceRNAs prediction
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ceRNA Network
The results page
FDR values are highlighted. Click on them for more details.
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ceRNA Network
The ceRNA network information page
Link to NCBI nucleotide database
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Protein-RNA
① protein-lncRNA interactions.
The query page
Select a RBP and a gene symbol(Optional)
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Protein-RNA
① protein-lncRNA interactions.
The results page
The number of targetSites are highlighted. Click on them for more details.
Export all query results as excel format
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Protein-RNA
① protein-lncRNA interactions.
The RNA-binding protein information page
Link to experiments sources information
Display the location in the deepView genome browser
Link to NCBI nucleotide database
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Protein-RNA
② protein-mRNA interactions.
The query page
The results and target information page are omitted because the interfaces are similar to the ones of protein-lncRNA interactions
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Protein-RNA
③ protein-pseudogene interactions.
The query page
The results and target information page are omitted because the interfaces are similar to the ones of protein-lncRNA interactions
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Protein-RNA
④ protein-sncRNA interactions.
The query page
The results and target information page are omitted because the interfaces are similar to the ones of protein-lncRNA interactions
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Functional Annotation
① miRFunction.
The query page
Multiple miRNAsselection are available
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Functional Annotation
① miRFunction.
The results page
Up to 13 categories of function prediction using enrichment analysis
Running parameters set in the query page
The union of has-miR-33a-5p & has-miR-615-3p target genes
Every category of function prediction can be expanded/collapsed by the fold button in the table headers
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Functional Annotation
② ceRNAFunction.
The query page
Gene symbol is required to enter
The same as the interface of ceRNA Network
The FDR threshold value of enrichment analysis
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Functional Annotation
② ceRNAFunction.
The results page
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Browser
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Browser
miRNAtarget tracks
link to UCSC
tracks options
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Download
Link to PubMed Download BED files containing CLIP clusters data
Search the data listed in the table
starBase v2.0 download center.
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Contact Us
For any comments and suggestions on the starBase v2.0 platform, please contact us.