Searching the database

CGCDB provides two types of searches:

1) A user can search for coexpressed partners for a gene of interest
2) A user can also determine which genes in the database are correlated to growth rate or cell specific productivity .
Note: The user can also browse the database by gene here

(A) To return gene-gene coexpression enter Entrez ID or Gene Symbol of your gene of interest (i.e. 17869 or MYC). In the case of gene phnotype correlations either growth or cell specific productivity must be selected
(B) Correlation measure type (either Pearson or Spearman; for details see Question #3 under “FAQ”)
(C) Correlation cut-off (0.5-0.95; for details see Question #2 under “FAQ”)
(D) Correlation direction of interest (Negative, Positive or Both)
(E) If connections between “child” genes (i.e. genes coexpressed with the gene of interest) are also relevant, select “Yes” for Internode connections; otherwise leave at default (“No”).
(F) Click “Submit” to generate a network graph for the selected Gene-gene coexpression. Selecting reset returns the search box to the default

Figure 1: Searching the database

Results output

Once the search has been completed those genes that correlate with the gene of or bioprocess phenotype above the selected threshold are returned. The results are shown in an interactive network diagram (only the top 20 correlated are shown for clarity), in addition the results are presented in tabular format (all correlated genes).

(A) The gene or bioprocess phenotype lies at the center of the netowrk and assigned a different color.
(B) Each correlated gene is shown. upon mouse over the gene title along with GO information is presented in the information box (D) The user can construct a new netowrk for a correlated gene by selecting the information box link(F)
(C)Upon user mouse over of a connecting edge the respective correlation is displayed int the information box (D) .
(E) The user can change the parameters of the current network
(G) Coexpression network tabular results. The user can link to the Entrez gene record for mouse (H). In addition the user can analyse coexpression patterns for a gene through coexpressDB (I). The table can be ordered ascending/descending for each column included the correlation coefficent (J).

Figure 2: Results output