ileS1 Pseudomonas fluorescens P18330

Help: filtering, analyzing and downloading annotation

1 Filtering Annotations

The filters beneath each of the column headings in annotation table can be clicked to specify filtering parameters, or to map annotations to sequence identifier types other than UniProtKB accessions. More advanced queries can be entered into the 'Advanced' text box.

2 Viewing Annotation Statistics

Statistics on the selected annotation set are available in the numbers adjacent to the 'Statistics' header.

3 Viewing Annotations

The annotation table defaults to displaying an initial 25 annotations, however this can be increased by changing the value adjacent to the 'Sample size' header. Alternatively, clicking the arrow at the bottom of the annotation table will advance the display to the next 25 annotations. Many of the values in the annotation table can be clicked on, and will provide further information and navigation options (this includes GO terms and sequence identifiers).

4 Downloading Annotations

An entire set of annotations can be downloaded in a text file from QuickGO by selecting 'Association format'. Users can select the file compression option (gzip) and the number of annotations to include.

Columns:

Alt

Symbol

Taxon

Qualifier

GO ID

GO Term name

Reference

With

Date

From

1 Filter:

Show:

Selected annotation

List proteins in selected annotation

All annotation to proteins in selected annotation

Columns shown:

splice

Symbol

Qualifier

GO ID

Reference

Evidence

With

Aspect

Name

Synonym

Type

Taxon

Taxon Name

Date

Source

GO Name

PubMed

RowID

Sequence

Choose the columns to be shown and click:

Choose protein identifier database

Use this filter to change between different sequence identifier types. QuickGO's default is to show annotations to UniProtKB (Swiss-Prot and TrEMBL) accession numbers.

UniProtKB - UniProtKB

UniProtKB/Swiss-Prot - UniProtKB/Swiss-Prot

UniProtKB/TrEMBL - UniProtKB/TrEMBL

IPI - IPI

dictyBase - dictyBase

EcoCyc - EcoCyc

EMBL - EMBL

ENSEMBL - ENSEMBL

FB - FB

GeneDB_Spombe - GeneDB_Spombe

GeneID - GeneID

GR - GR

TIGR_CMR - TIGR_CMR

MGI - MGI

RefSeq - RefSeq

TAIR - TAIR

UniGene - UniGene

WB - WB

ZFIN - ZFIN

QuickGO maps between different identifier types by using a combination of mapping files provided by the databases, and using identifier cross-references supplied by UniProtKB.

If more than one identifier type needs to be used to map all required sequences, drag the selected databases to change the order in which identifiers are found.

Filter annotations by protein IDs from any database:

QuickGO will map identifiers to UniProtKB accession numbers unless you have specified an alternative identifier type via the 'DB' filter box.

OR - select a list of proteins:

BHF-UCL

KRUK

ReferenceGenome

Filter by taxonomy

To filter by species/taxonomic group, list taxon identifiers in the text box or select one of the pre-defined taxonomic groups below.

	9606	Human
	10090	Mouse
	40674	Mammalia
	3398	Magnoliophyta (flowering plants)
	2759	Eukaryota
	1117	Cyanobacteria

Visit NEWT to find identifiers for other taxonomic groups

Qualifier:

(none)

colocalizes_with

contributes_to

NOT

NOT|colocalizes_with

NOT|contributes_to

GO Terms:

Enter a list of GO identifiers (GO:nnnnnnn), separated by space, comma or newline characters

Use these terms as a GO slim

Select the set of relationships to be applied when slimming up annotations to the selected GO term set:

Default behaviour (is_a and part_of relationships only)

is_a only

is_a, part_of, regulates, positively_regulates and negatively_regulates

Use all relationships

Custom

Find annotations that directly associate the selected terms

Find annotations to descendants of these terms (annotations will display the original GO terms applied)

Annotated from any of these references:

GO_REF:*

GO Reference

GO_REF:0000002

InterPro2GO

GO_REF:0000003

EC2GO

GO_REF:0000004

Swiss-Prot Keywords2GO

GO_REF:0000019

Compara

GO_REF:0000020

HAMAP2GO

GO_REF:0000023

Subcellular Location2GO

References (with or without database prefix):

With evidence:

IMP,IGI,IPI,IDA,IEP,EXP

Manual Experimental

IMP,IGI,IPI,IDA,IEP,EXP,ISS,TAS,NAS,ND,IC,RCA

Manual All

IMP

inferred from mutant phenotype

IGI

inferred from genetic interaction

IPI

inferred from physical interaction

IGC

Inferred from Genomic Context

ISS

inferred from sequence or structural similarity

IDA

inferred from direct assay

IEP

inferred from expression pattern

IEA

inferred from electronic annotation

TAS

traceable author statement

NAS

non-traceable author statement

no data

inferred by curator

RCA

reviewed computational annotation

ISA

inferred from sequence alignment

EXP

inferred from experiment

Annotated with reference:

EC:*

Enzyme Code

HAMAP:*

High-quality Automated and Manual Annotation of microbial Proteomes

InterPro:*

InterPro

SP_KW:*

UniProt Knowledgebase keywords

SP_SL:*

UniProtKB Subcellular Location identifiers

UniProtKB:*

UniProtKB

Annotated with (with or without database prefix):

Assigned by

Select annotation from:

AgBase

BHF-UCL

dictyBase

DictyBase

EcoCyc

Encyclopedia of E. coli metabolism

EcoliWiki

EcoliWiki from EcoliHub

ENSEMBL

Ensembl

FlyBase

GDB

The GDB Human Genome Database

GeneDB_Spombe

GeneDB Schizosaccharomyces Pombe

GRAMENE

HGNC

HGNC curators

HPA

Human Proteome Atlas

IntAct

LIFEdb

MGI

Mouse Genome Informatics

PINC

Proteome Inc via Locuslink

Reactome

RGD

Rat Genome Database

Roslin_Institute

Roslin Institute curators

SGD

Saccharomyces Genome Database

TAIR

The Arabidopsis Information Resource

TIGR

The Institute of Genome Research

UniProtKB

WormBase

ZFIN

The Zebrafish Information Network

Advanced search

View annotation:

Columns:

Alt

Symbol

Taxon

Qualifier

GO ID

GO Term name

Reference

With

Date

From

Sample size:

4 Download

Options: gzip: limit:

Format: . Current columns, Tab Separated Values: .

Web service: annotation

Use this URI template to access this data as a service:

GAnnotation?format=tsv&limit=max-number-of-rows{&gz}{&q=advanced query}{&field=value{,value}}

Full details can be found on the QuickGO Web Services page.