Database for Annotation Visualization and Integrated Discovery DAVID

Database for Annotation, Visualization and Integrated Discovery (DAVID ) Ø Functional Annotation Tool l l Gene Ontology Protein interaction Protein domain Pathway Disease Ø Gene ID Conversion Ø Gene Functional Classification

DAVID 操作流程 上傳基因列表到網站 Gene Name Batch Viewer Gene Functional Classification Functional Annotation Tool 選定類別以進行分析 取得結果

上傳基因列表 AFFYMETRIX_3 PRIME_IVT_ID AFFYMETRIX_EXON_GENE_ID AFFYMETRIX_SNP_ID AGILENT_CHIP_ID AGILENT_OLIGO_ID ENSEMBL_GENE_ID ENSEMBL_TRANSCRIPT_ID ENTREZ_GENE_ID FLYBASE_TRANSCRIPT_ID GENBANK_ACCESSION GENOMIC_GI_ACCESSION GENPEPT_ACCESSION ILLUMINA_ID IPI_ID MGI_ID OFFICIAL_GENE_SYMBOL PFAM_ID PIR_ID PROTEIN_GI_ACCESSION REFSEQ_GENOMIC REFSEQ_MRNA REFSEQ_PROTEIN REFSEQ_RNA RGD_ID SGD_ID TAIR_ID UCSC_GENE_ID UNIGENE UNIPROT_ACCESSION UNIPROT_ID UNIREF 100_ID WORMBASE_GENE_ID WORMPEP_ID ZFIN_ID Not Sure

Functional Annotation Tool DAVID Gene ID: It is an internal ID generated on "DAVID Gene Concept" in DAVID system. One DAVID gene ID represents one unique gene cluster belonging to one single gene entry. 1. Input Gene list : 817 Map to David Database : 754 David IDs : 734 2. Genes from your list involved in this annotation categories 3. 99 / 734 4. Single chart report only for this annotation categories.

Functional Annotation Chart Report is an annotation-term-focused view which lists annotation terms and their associated genes under study. To avoid over counting duplicated genes, the Fisher Exact statistics is calculated based on corresponding DAVID gene IDs by which all redundancies in original IDs are removed. All result of Chart Report has to pass the thresholds (by default, Max. Prob. <=0. 1 and Min. Count>=2) in Chart Option section to ensure only statistically significant ones displayed. List Total(LT) - number of genes in the gene list mapping to the category of which the term is a member Population Hits(PH) - number of genes in the background gene list mapping to a specific term Population Total(PT) - number of genes in the background gene list mapping to the category 每頁可顯示多少結果 RT (Related Term) Related Term Search can identify other similar terms a modified Fisher Exact P-Value (EASE Score)

RT (Related Term) Any given gene is associating with a set of annotation terms. If genes share similar set of those terms, they are most likely involved in similar biological mechanisms. The algorithm adopts kappa statistics to quantitatively measure the degree of the agreement how genes share the similar annotation terms. Kappa result ranges from 0 to 1. The higher the value of Kappa, the stronger the agreement. Any a biological process/term coming from all functional categories listed in DAVID.

Annotation Category - Functional Categories COG_ONTOLOGY refers to an ontology from NCBI's COG database The database of Clusters of Orthologous Groups of proteins (COGs): a tool for genome-scale analysis of protein functions and evolution SP_PIR_KEYWORDS are keywords defined by the Swiss. Prot/Uniprot and PIR (Protein Information Resource) UP_SEQ_FEATURE refers to the annotation category, Uniprot Sequence Feature, found at the Uniprot site, within their report.

Annotation Category – Protein domain & Protein Interaction Protein structure

Annotation Category - Gene Ontology GOTerms are categorized into 3 groups: BP - Biological Process MF - Molecular Function CC - Cellular Component GOTERM_BP_1 -> GO term under Biological Process (BP) in the Level 1. GOTERM_BP_ALL -> GO term under Biological Process (BP) in the ALL possible Levels. GOTERM_BP_FAT - Basically this test exams the significance of enriched annotation (GO FAT) filters out very broad GO terms based on a measured specificity of each term (not level-specificity)

Annotation Category-Pathways KEGG Biocarta

Combined View Annotation 總共 11項 Categories 挑選 11項 Categories

Functional Annotation Clustering Due to the redundant nature of annotations, Functional Annotation Chart presents similar/relevant annotations repeatedly. It dilutes the focus of the biology in the report. To reduce the redundancy, the newly developed Functional Annotation Clustering report groups/displays similar annotations together which makes the biology clearer and more focused to be read vs. traditional chart report. • The Functional Annotation Clustering integrates the same techniques of Kappa statistics to measure the degree of the common genes between two annotations, and fuzzy heuristic clustering to classify the groups of similar annotations according kappa values. 調整 Kappa statistics 的參數 調整 fuzzy heuristic clustering的參數 P_value All gene involved in this annotation cluster Heat map Ease score (modified fisher exact test)

Initial Group Members (any value >=2; default = 4): the minimum gene number in a seeding group, which affects the minimum size of each functional group in the final. In general, the lower value attempts to include more genes in functional groups, particularly generates a lot small size groups. Final Group Members (any value >=2; default = 4): the minimum gene number in one final group after “cleanup” procedure. In general, the lower value attempts to include more genes in functional groups, particularly generates a lot small size groups. It co-functions with previous parameters to control the minimum size of functional groups. In the final cluster, the number of terms that a cluster must have to be presented in the output. Multi-linkage Threshold (any value between 0% to 100%; default = 50%): It controls how seeding groups merge each other, i. e. two groups sharing the same gene members over the percentage will become one group. The higher percentage, in general, gives sharper separation i. e. it generates more final functional groups with more tightly associated genes in each group. In addition, changing the parameter does not contribute extra genes into unclustered group. Enrichment Score = [ -log(P_value 1) + -log(P_value 2) + -log(P_value N) ] / n

Chart vs Cluster • If you run both functions with defualt setting, they will not be totally overlapped. In general, clustering result may contain more result than chart. In clustering, some 'non-significant' terms could be included due to the link of their 'significant' neigthbors (co-members in on cluster). • If you want to completely cross link the two reports, you should run chart report by setting p-value cutoff to "1" (ground level). Thus, you will have all possible terms with significant or insignificant pvalues.

上傳基因列表到網站 Gene Name Batch Viewer Gene Functional Classification Functional Annotation Tool 選定類別以進行分析 取得結果

Another Tools in DAVID

Gene Name Batch Viewer

Gene Functional Classification Tool Term report

Gene Functional Classification Tool - Create sublist

Gene ID Conversion Tool

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