EXAMPLE APPLICATION: VvEXPA14 (VIT_13s0067g02930) co-expression network
EXAMPLE APPLICATION: VvEXPA14 (VIT_13s0067g02930) co-expression network
As VvEXPA14 is placed on Chr13, download the corresponding zipped file and extract the folder with the VIT code: VIT_13s0067g02930. In this example, there are three files: i. Co-expressed gene information and enrichment analysis results (FDR < 0.05) for ii. MapMan BIN functional categories and iii. select cis-regulatory elements.Table 1: The top 10 co-expressed genes of VvEXPA14 and relevant information. See raw file for the full list.
As VvEXPA14 is placed on Chr13, download the corresponding zipped file and extract the folder with the VIT code: VIT_13s0067g02930. In this example, there are three files: i. Co-expressed gene information and enrichment analysis results (FDR < 0.05) for ii. MapMan BIN functional categories and iii. select cis-regulatory elements.Table 1: The top 10 co-expressed genes of VvEXPA14 and relevant information. See raw file for the full list.
Query = 12xV1 code for the query gene
Target = 12xV1 code of the co-expressed gene
Frequency = Frequency of co-expression interaction(s) present across individual GCNs
Condition = ID of experiment where the co-expression interaction is top-ranked (i.e. top 300) and the corresponding PCC value of the interaction
Function_Vnet = VitisNet annotation of co-expressed target
Network_Vnet = VitisNet classification of co-expressed target
BIN = MapMan BIN classification of co-expressed target
Query = 12xV1 code for the query gene
Target = 12xV1 code of the co-expressed gene
Frequency = Frequency of co-expression interaction(s) present across individual GCNs
Condition = ID of experiment where the co-expression interaction is top-ranked (i.e. top 300) and the corresponding PCC value of the interaction
Function_Vnet = VitisNet annotation of co-expressed target
Network_Vnet = VitisNet classification of co-expressed target
BIN = MapMan BIN classification of co-expressed target
Table 2: The top 10 enriched MapMan BIN functional category of VvEXPA14 gene co-expression network. See raw file for the full list.
Table 2: The top 10 enriched MapMan BIN functional category of VvEXPA14 gene co-expression network. See raw file for the full list.
match_in_group = # of genes with associated annotation in group
group_size = Total # of genes with annotation in group
match_in_bg = Total # of genes with annotation in genome
bg_size = Total # of genes with annotation in genome
p_val = Calculated P-value
adj_p_val(FDR) = Adjusted P-value (False Discovery Rate)
BIN_ID = MapMan BIN ID of enriched functional category
BIN_KW = MapMan BIN description of enriched functional category
Hits = IDs of gene with associated annotation in group (Note: Only the first four hits is displayed here)
match_in_group = # of genes with associated annotation in group
group_size = Total # of genes with annotation in group
match_in_bg = Total # of genes with annotation in genome
bg_size = Total # of genes with annotation in genome
p_val = Calculated P-value
adj_p_val(FDR) = Adjusted P-value (False Discovery Rate)
BIN_ID = MapMan BIN ID of enriched functional category
BIN_KW = MapMan BIN description of enriched functional category
Hits = IDs of gene with associated annotation in group (Note: Only the first four hits is displayed here)
Table 3: Enriched cis-regulatory elements (CRE) in the promoters (1kb upstream) of VvEXPA14 co-expressed genes. See raw file for the full list.
match_in_sample = # of genes with associated CRE in group
sample_size = Total # of genes with associated CRE in group
match_in_genome = Total # of genes with associated CRE in genome
genome_size = Total # of genes with associated CRE in genome
p_val = Calculated P-value
adj_p_val(FDR) = Adjusted P-value (False Discovery Rate)
motif = Name of enriched CRE
motif_ID = ID of enriched CRE
TF family = TF family classification of enriched CRE
Hit = IDs of gene with enriched CRE in group (Note: Only the first four hits is displayed here)
Table 3: Enriched cis-regulatory elements (CRE) in the promoters (1kb upstream) of VvEXPA14 co-expressed genes. See raw file for the full list.
match_in_sample = # of genes with associated CRE in group
sample_size = Total # of genes with associated CRE in group
match_in_genome = Total # of genes with associated CRE in genome
genome_size = Total # of genes with associated CRE in genome
p_val = Calculated P-value
adj_p_val(FDR) = Adjusted P-value (False Discovery Rate)
motif = Name of enriched CRE
motif_ID = ID of enriched CRE
TF family = TF family classification of enriched CRE
Hit = IDs of gene with enriched CRE in group (Note: Only the first four hits is displayed here)