GO enrichment analysis     More powerful tools, please visit (Dynamic GO enrichment analysis)





Select a file Example

Which wanted to study gene list, each row id first as a gene, gene id in the table to include in the genetic background
     






We provide references of rice, Arabidopsis thaliana, mice, rat, zebra fish, caenorhabditis elegans, gallus, drosophila melanogaster, and homo sapiens. You can choose gene ID or transcript ID according to your gene set ID. You can click “Browse reference” to view the IDs.
Select a file Example

Of all genes GO annotation files, format as the first listed as gene id, the second to GO annotation results
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GO enrichment analysis, a tutorial

Function:
Gene Ontology (GO) is an international standardized gene functional classification system which offers a dynamic-updated controlled vocabulary and a strictly defined concept to comprehensively describe properties of genes and their products in any organism. GO has three ontologies: molecular function, cellular component and biological process. The basic unit of GO is GO-term. Each GO-term belongs to a type of ontology. GO functional analysis provides not only GO functional annotations of a given gene set, but also GO enrichment analysis of the given gene set that correspond to biological functions. Firstly all genes in the given gene set are mapped to GO terms in the Gene Ontology database, and gene numbers are calculated for every term. Then significantly enriched GO terms in the given gene set comparing to the genome background are defined by hypergeometric test. The calculating formula of P-value is:
生物云平台 Here N is the number of all genes with GO annotation; n is the number of genes in the given gene set in N; M is the number of all genes that are annotated to a certain GO term; m is the number of genes in the given gene set in M. The calculated p-value is then gone through FDR Correction, taking FDR ≤ 0.05 as a threshold. GO terms meeting this condition are defined as significantly enriched GO terms in the gene set.


Input:

①File format: a tab delimited text file. If your data is not TAB delimited, you can use Excel to convert it.you can also enter two columns,the second column is the multiple of multiple log2, greater than 0 up, less than 0 down

②Gene set: genes need enrichment analysis. Gene IDs must be separated by new lines and included in the background set.

③ Background set: For model organism, pre-compiled references are available, including rice, Arabidopsis thaliana, mice, rat, zebra fish, caenorhabditis elegans, gallus, drosophila melanogaster, and homo sapiens. Gene ID and transcript ID are optional according to your gene set IDs.
For other organism, you need to upload a background set with GO IDs. There are two types of file formats: the first column is gene names, and the second column is GO ID; or the first column is gene names while other columns are GO IDs of this gene. For example::

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Output:

①out.[PFC].html: enrichment results of three ontologies in html.

②out.[PFC].xls: enrichment results of three ontologies in excel.

③out.[PFC].png:directed acyclic graph of GO functions.

④out.secLevel2.svg/png:histogram of second level GO terms.

⑤out.level2.xls: statistics table of second level GO terms.

Example:GO enrichment purpose gene list file   example file of description
GO enrichment purpose gene list file2   example file of description
Output:

① out.[PFC].html Web page format as a result, the three corresponding GO three main categories. The results shown in the figure below, Consists of two parts: The first part is the GO enrichment results TAB, including the GOid, GO functional description, proportion of genes, genetic background proportion, P, Q, Q P value is less than 0.05 the display of the red.
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② The second part for the enrichment of the GO specific genes, click GOid can link to http://amigo.geneontology.org website, you can see the GO.
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③ out.[PFC].png,out.[PFC].pdf,out.[PFC].xls GO enrichment of directed acyclic graph, show only the enrichment of the GO term (that is, the p value is less than 0.05), no less than 0.05 results, would not have these files. In XLS results from view, corresponding with the web, including GOid, GO functional description, proportion of genes, genetic background proportion, P, Q, and the corresponding gene id.


④ out.secLevel.svg/png Images results as shown in the figure below, to GO the secondary classification statistical figure, the statistics for enrichment of genes in the second category of number of each classification, statistical results in the XLS table. Form content including, Ontology, Class secondary classification (GO), number of genes, the specific gene id.生物云平台 生物云平台