RiceFREND Ver 2.0 User Manual

Transcription

1 RiceFREND Ver 2.0 User Manual About Coexpression Index Coexpression Search Options Coexpression Gene Network in Hyper Tree Coexpression Gene Network in Cytoscape Web (Single) Coexpression Gene Network in Cytoscape Web (Multiple) Coexpression Gene Network in Graphviz Mutual Rank (MR) List Analysis Tool: GO Enrichment Test Analysis Tool: Cis-Element Analysis P2 P3 P4 P5 P6 P7 P8 P9 P10 P1

2 About Coexpression Index RiceFREND uses Mutual Rank (MR) as an index for coexpression as described in ATTED-II. Obayashi and Kinoshita (2009) DNA Res. 16: Obayashi et al. (2009) Nucleic Acids Res. 37:D PCC rank is assigned based on descending order of PCC value; for example, the PCC rank of Gene C to Gene A is 3 and that of Gene A to Gene C is 4. The MR between Gene A and Gene C is the geometric average of the ranks. As an alternative index for coexpression, we also use MR rank, which is assigned based on ascending order of MR values. P2

3 Search Options Enter keyword(s). See help for options. Initiate search from aligned loci in each chromosome. Enter keyword(s). See help for options. 1. Select 2 or more guide genes. 2. Set Hierarchy and MR/Rank 3. Click Draw to generate network. Search results in tabular format. Link to MSU annotation OS ID and links to RAP, RiceXPro, SALAD Link to genes coexpressed with guide gene in HyperTree (P4). MR list of genes coexpressed with guide gene (P8). Matrix data shows MR information of guide genes. Select guide genes directly from panel to perform Multiple Guide Gene Search. P3

4 Coexpressed Gene Network in HyperTree Select network size by defining MR and Hierarchy. This list provides information on nodes in gene network. Node label options: Locus ID Gene Symbol Gene Name Transcription Factor MSU ID KEGG Pathway Select 2 or more genes to perform Multiple Guide Gene Search. Genes assigned in KEGG pathway Select other network viewers: Cytoscape Web (P5) Graphviz (P7) The list provides direct link to KEGG database and option to highlight nodes with a specific pathway. Analysis Tools: GO Enrichment Test (P9) Cis-element Analysis (P10) Download options Node List Cytoscape Data P4

5 Coexpressed Gene Network in Cytoscape Web Single Guide Gene Search Select network size by defining MR and Hierarchy. Node label options: Locus ID Gene Symbol Gene Name Transcription Factor MSU ID KEGG Pathway Graph layout options: Force Directed Radial Tree Circle Compound Spring Embedder Highlight all KEGG pathways Select other network viewers: Graphviz (P7) Download options Node List Cytoscape Data The list provides direct link to KEGG database and option to highlight nodes with a specific pathway. Scale up or scale down. Scroll the image. P5

6 Coexpressed Gene Network in Cytoscape Web Multiple Guide Gene Search Select network size by defining MR / Rank and Hierarchy. Node label options: Locus ID Gene Symbol Gene Name Transcription Factor MSU ID KEGG Pathway Graph layout options: Force Directed Radial Tree Circle Compound Spring Embedder Highlight all KEGG pathways Select other network viewers: HyperTree (P4) Graphviz (P7) The list provides direct link to KEGG database and option to highlight nodes with a specific pathway. Scale up or scale down. Scroll the image. Download options: Node List Cytoscape Data P6

7 Coexpressed Gene Network in Graphviz Select network size by defining MR/Rank and Hierarchy. Layout Type options: Symmetric Radial Hierarchical Select image size. The list provides direct link to KEGG database and option to highlight nodes with a specific pathway. P7

8 Mutual Rank (MR) List 1. Select Top genes from list or specific locus 2. Perform GO Enrichment Test (P9), Cis-element Analysis (P10) or Multiple Guide Gene Search (P6) on selected genes Extract gene(s) of interest from MR List by filtering P8

9 GO Enrichment Test Fisher s exact test is applied to GO Enrichment Test, thereby providing tabular list of statistically enriched GO terms with p-value adjusted by Benjamini and Hochberg s method for multiple testing corrections. The result also be viewed in graph format with filter opnon. In the case of Filter on, graph can be drawn against GO terms with caseposinve value above 5 Search domain options: Biological Process Molecular Function Graph Tabular List P9

10 Cis-element Analysis This test statistically identifies the presence of user defined cis-element in 1kb up-stream region of coexpressed genes based on chi-square test, Fisher s exact test and G-test. Enter cis-element query sequence. P10