File S1 - Representing Kidney Development Using the Gene Ontology

File S1. includes Tables S1 to S9 presented in separate tabs of an Excel spreadsheet, representing the input gene product list and the output of the GO term enrichment analyses from GO-Elite and Ontologizer Enrichment tools using the 2009 and 2012 annotation and Gene Ontology datasets for the differentially expressed gene products in the Baelde 2004 study. A description tab entitled ‘Tables S2–S9 Description’, has been included, defining the output from the GO-Elite and Ontologizer GO term enrichment tools presented in Tables S2–S9. Table S1. Input protein list. Mapping of the gene product identifiers from the Baelde 2004 study to UniProtKB accession numbers. Most of the differentially expressed gene products in DN glomeruli were mapped to a UniProtKB accession number and those that could not be mapped were not annotated and are not included in the table. Table S2. GO-Elite analysis on up-regulated proteins in DN glomeruli, using the 2009 Gene Ontology and annotation sets. Results from the GO-Elite enrichment analysis tool on the up-regulated proteins from the Baelde using the Gene Ontology and Annotation files from March 2009; showing significantly enriched GO terms. The boldface terms are referred to in the manuscript text. The “Study” column shows the number of proteins in the input list with an annotation to the given term. The “Population” column shows the number of proteins in the background list with an annotation to the given term. Table S3. Ontologizer analysis on up-regulated proteins in DN glomeruli, using the 2009 Gene Ontology and annotation sets. Results from the Ontologizer enrichment analysis tool on the up-regulated proteins from the Baelde list, using the Gene Ontology and Annotation files from March 2009; showing significantly enriched GO terms. The boldface terms are referred to in the manuscript text. The “Population” column shows the number of proteins in the background list with an annotation to the given term. The “Study” column shows the number of proteins in the input list with an annotation to the given term. Table S4. GO-Elite analysis on down-regulated proteins in DN glomeruli, using the 2009 Gene Ontology and annotation sets. Results from the GO-Elite enrichment analysis tool on the down-regulated proteins from the Baelde list, using the Gene Ontology and Annotation files from March 2009; showing significantly enriched GO terms. The “Study” column shows the number of proteins in the input list with an annotation to the given term. The “Population” column shows the number of proteins in the background list with an annotation to the given term. Table S5. Ontologizer analysis on down-regulated proteins in DN glomeruli, using the 2009 Gene Ontology and annotation sets. Results from the Ontologizer enrichment analysis tool on the down-regulated proteins from the Baelde list, using the Gene Ontology and Annotation files from March 2009; showing significantly enriched GO terms. The boldface terms are referred to in the manuscript text. The “Population” column shows the number of proteins in the background list with an annotation to the given term. The “Study” column shows the number of proteins in the input list with an annotation to the given term. Table S6. GO-Elite analysis on up-regulated proteins in DN glomeruli, using the 2012 Gene Ontology and annotation sets. Results from the GO-Elite enrichment analysis tool on the up-regulated proteins from the Baelde list, using the Gene Ontology and Annotation files from March 2012; showing significantly enriched GO terms. The boldface terms are referred to in the manuscript text and the italicized boldface indicates new terms created during the Renal GO Annotation Initiative. The “Study” column shows the number of proteins in the input list with an annotation to the given term. The “Population” column shows the number of proteins in the background list with an annotation to the given term. Table S7. Ontologizer analysis on up-regulated proteins in DN glomeruli, using the 2012 Gene Ontology and annotation sets. Results from the Ontologizer enrichment analysis tool on the up-regulated proteins from the Baelde list, using the Gene Ontology and Annotation files from March 2012; showing significantly enriched GO terms. The boldface terms are referred to in the manuscript text and the italicized boldface indicates new terms created during the Renal GO Annotation Initiative. The “Population” column shows the number of proteins in the background list with an annotation to the given term. The “Study” column shows the number of proteins in the input list with an annotation to the given term. Table S8. GO-Elite analysis on down-regulated proteins in DN glomeruli, using the 2012 Gene Ontology and annotation sets. Results from the GO-Elite enrichment analysis tool on the down-regulated proteins from the Baelde list, using the Gene Ontology and Annotation files from March 2012; showing significantly enriched GO terms. The boldface terms are referred to in the manuscript text and the italicized boldface indicates new terms created during the Renal GO Annotation Initiative. The “Study” column shows the number of proteins in the input list with an annotation to the given term. The “Population” column shows the number of proteins in the background list with an annotation to the given term. Table S9. Ontologizer analysis on down-regulated proteins in DN glomeruli, using the 2012 Gene Ontology and annotation sets. Results from the Ontologizer enrichment analysis tool on the down-regulated proteins from the Baelde list, using the Gene Ontology and Annotation files from March 2012; showing significantly enriched GO terms. The boldface terms are referred to in the manuscript text and the italicized boldface indicates new terms created during the Renal GO Annotation Initiative. The “Population” column shows the number of proteins in the background list with an annotation to the given term. The “Study” column shows the number of proteins in the input list with an annotation to the given term.
(XLSX)