starBase v2.0 Tutorial

© 2010-2013, Jianhua Yang at Sun Yat-sen University

For comments, suggestions on the starBase platform, please contact us: lsp03yjh@gmail.com

On commercial use, contact: yangjh7@mail.sysu.edu.cn

Cover Pan-Cancer Analysis

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

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.

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

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

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

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

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

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

miRNA-lncRNA

① miRNA-lncRNA interactions.

The target information page

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

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

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

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.

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

miRNA-mRNA

① miRNA-target intersections.

The target information page

miRNA-mRNA

Choose the interested clade, genome and assembly

Select a microRNA and a gene symbol

② miRNA-mRNA interactions.

The query page

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

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

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

ceRNA Network

The results page

FDR values are highlighted. Click on them for more details.

ceRNA Network

The ceRNA network information page

Link to NCBI nucleotide database

Protein-RNA

① protein-lncRNA interactions.

The query page

Select a RBP and a gene symbol(Optional)

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

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

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

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

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

Functional Annotation

① miRFunction.

The query page

Multiple miRNAsselection are available

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

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

Functional Annotation

② ceRNAFunction.

The results page

Browser

Browser

miRNAtarget tracks

link to UCSC

tracks options

Download

Link to PubMed Download BED files containing CLIP clusters data

Search the data listed in the table

starBase v2.0 download center.

Contact Us

For any comments and suggestions on the starBase v2.0 platform, please contact us.