Therefore, each node in the network was colorized red (indicating wild-type) based on the color settings in ClueGO. When I created the network comparing wild-type profile 45 and dCIN5 profile 45 gene IDs, every functional category was more highly overrepresented in the wild-type strain than the dCIN5 strain.Therefore, the number of genes belonging to the specific functional category could be the same for each node. I downloaded the plugin and used it to determine the percentages of wt and dCIN5 genes were part of the functional categories in the network, but each pie chart showed the same percentages. There is a ClueGO plugin that gives the option to make the nodes of the network pie charts, giving information about the percentage of genes in each cluster that are part of the specific functional group.Gene IDs offer the creation of a network, but the gene ontology terms only create separate nodes with no edges. There is the option of using gene list IDs or gene ontology terms for the analysis.Only the categories that are common to all sets of genes are included in the network. ClueGO does not allow for unique gene ontology groups to be included in the network.Present a Journal Club on "Physiological and Transcriptional Responses of Anaerobic Chemostat Cultures of Saccharomyces cerevisiae Subjected to Diurnal Temperature Cycles".Try to figure out CompGO and how to use the R software.Run ClueGO with Cytoscape and create powerpoint of various functions it can do.It offers information about which inputs are unique to either list and those that are overlapping. Allows you to input sets of data and compare them.Allows for the comparison of gene ontology terms to determine which are overlapping and which are unique between the strains.Does not indicate which terms are overlapping or unique.InteractiVenn- Allows for the creation of a venn diagram for up to six sets of data.Pangloss- Creates a venn diagram from only two lists of data, but states which terms are overlapping and which are unique.Allows for the visualization of the gene ontology groups with a bar chart, multiple pie diagram, overlaid area chart of difference, and bar chart of difference.(Gives the option of using Bonferroni corrected p-values) Panther Compare Lists- Allows for a comparison between gene ID lists.May need to request access to use the software. " It is possible to compare arbitrarily selected organisms or groups of organisms from the taxonomic tree on the basis of the functionality of their genes" (GO Tools: Visualization).GOTaćxplorer- Allows for the comparison between gene sets.Determines which gene ontology categories are overrepresented in the gene list.BiNGO- Cytoscape plug-in that creates networks of the gene ontologies.Limited species inclusion: Bacteria, Virus, Zebrafish, Human, Rice.Comparative GO- "A webserver for comparative gene ontology, gene ontology network and gene ontology based gene selection".Need to figure out how to use CompGO in the R software. Dahlquist requested access to the plug-in. Requires Cytoscape, as it is a plug-in for the software.ClueGO- Creates networks from the gene ontology terms and allows for a comparison between two lists of data.You have to use the gene list, not the GO list from STEM.There is no option to restrict the GO terms based on p-value significance.Panther Classification System- Creates bar graphs or pie charts of the gene ontology terms from the gene list data from STEM.Need to determine how to change file format of GO list from STEM software to work on WEGO.WEGO- Creates comparative plots, but supports narrow file types.Therefore, it can be used only for a single strain. Does not allow for a comparison between GO lists.The resulting graphs colorize the functional groups according to the p-value. Revigo- Allows for the creation of scatterplots from a single list of gene ontology IDs, with the option of including p-values.Alice and Mihir May 28 Journal Club Powerpoint. Present a Journal Club on " Parameter Estimation for Gene Regulatory Networks from Microarray Data: Cold Shock Response in Saccharomyces cerevisiae".Organize STEM profile results for all strains to make comparison of the profile types.Perform an exploratory search for software that can be used for comparing gene ontologies of the wild-type, dCIN5, dGLN3, dHAP4, dHMO1, and dZAP1 strains of Saccharomyces cerevisiae.Wild-Type: wt_one_strain_ANOVA_out_data.xls.dZAP1: dZAP1_one_strain_ANOVA_out_data.xls.dHMO1: dHMO1_one_strain_ANOVA_out_data.xls.dHAP4: dHAP4_one_strain_ANOVA_out_data.xls.dGLN3: dGLN3_one_strain_ANOVA_out_data.xls.dCIN5: dCIN5_one_strain_ANOVA_out_data.xls.Microarray data for each of the strains used in the analysis:
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