DAVID Bioinformatics 6.7
The Database for Annotation, Visualization and Integrated Discovery
DAVID Bioinformatics Resources 6.7
National Institute of Allergy and Infectious Diseases (NIAID), NIH
list manager
Universial Gene List Manager Panel

1. Introduction

The information is stored in a centralized place so that any DAVID tools can cross-access them. Users do not need to re-submit the same gene list for different DAVID Tools. Therefore, the List Manager Panel is centralized and universial for all DAVID tools.

2. Upload Tab



Gene List Format: You can either load a gene list from a file or paste a gene list to the text box. DAVID was designed to accept the data starting from the first row without hearder (i.e. accession). The gene list has to be in a format of one gene in one row and only the first column is considered in the analysis. DAVID is case insensitive for all the accessions/IDs. Since DAVID list manager is centrilized, the format requirement to submit a gene list are the same for ALL DAVID tools. In addition, the submitted gene lists could be used as customized background genes in the enrichment analysis based on your choice at step 3. The indication of a successful submission is that you should see the corresponding gene lists listed by list tab or background tab. Moreover, an expected gene # should also associated with the gene lists.

About Step 3:  Gene List means the submitted genes are for annotation analysis. Usually they are users' interesting genes selected from experiment, e.g. genes with significant fold changes in an Affy array experiment. The gene list submitted as Gene List will show up in List Tab; Background means the submitted genes as a cutomized gene background are for enrichment background calculation purpose. This feature only is useful when all pre-built backgrounds in DAVID are not satisfied with users' particular purpose.Please read more how to use customized background. The gene list submitted as background will show up in Background Tab.

What are the demo_list 1 and demo_list 2? Demo_list 1 & 2 from our published Affy microarray studies
are pre-built gene lists for new users to easily get into and test DAVID functions.

An example:

Copy/paste IDs to "box A" -> Select Identifier as  "Affy_ID" -> List Type as "Gene List" -> Click "Submit" button

1007_s_at
1053_at
117_at
121_at
1255_g_at
1294_at
1316_at
1320_at
1405_i_at
1431_at
1438_at
1487_at
1494_f_at
1598_g_at


3. List Tab



Gene-Species Mapping Manager(top box):
After selecting a gene list from List Manager (bottom), this box specifically generates a  summary of gene-species  mapping. If the gene list contains multiple species, users can define one or multiple gene-species groups to analyze together/separately.

List Manager (bottom box):
Uers are allowed to input multiple gene list  in one web session.  Each gene input gene list is remembered and listed in this box. By default, the last input  gene list is the current list being selected and to be analyzed.

Special Note:
Clicking <<Use>> and <<Select>> buttons are required in order to make according switches.



4. Background Tab



Background Tab allows you to manage different background for enrichment analysis


Last edited: Jan. 2007




 Please cite Nature Protocols 2009; 4(1):44 & Nucleic Acids Res. 2009;37(1):1 within any publication that makes use of any methods inspired by DAVID.
                          

        

                 
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