Download Archive: 2014.03.07

ZFIN Data Reports from: 7 Mar 2014

Warranty Disclaimer and Copyright Notice

ZFIN data reports are updated every day of the week at 10:10pm PST with the exception of the externally hosted files. The format for each file is described below. All files use tab as the field delimiter. The 'Download File' link will display the file in your browser. Click the download button to save the file onto your local system (includes timestamp and header info). If you choose to link to a ZFIN data page from your web site, append the ZFIN ID to the URL http://zfin.org/
e.g. http://zfin.org/ZDB-GENE-980526-166
for the 'shha' gene. Please direct questions or requests for additional data to ZFIN.

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Column Headers

File Size

Number of Records

Anatomical Ontologies

Zebrafish Anatomy Term

Show

204 KB

2,858

Zebrafish Anatomy Term Relationships

Show

168 KB

5,396

Zebrafish Anatomy Term Synonyms

Show

90 KB

1,750

Zebrafish Development Stage Terms

Show

315 KB

13,380

Zebrafish Stage Series

Show

2 KB

Antibody Data

Antibodies

Show

116 KB

1,457

Antibody Expressions in wild-type

Show

253 KB

4,560

Fish

Fish Components

Show

10 MB

61,447

Gene Expression

Expression data for wildtype fish

Show

24 MB

152,304

1	2	3	4	5	6	7	8	9	10	11	12	13
Gene ID	Gene Symbol	Genotype	Super Structure ID	Super Structure Name	Sub Structure ID	Sub Structure Name	Start Stage	End Stage	Assay	Publication ID	Probe ID	Antibody ID

Expression Environment Description

Show

536 KB

8,428

Expression Experiment-Figure

Show

14 MB

249,626

Zebrafish Gene Expression by Stage and Anatomy Term

Show

22 MB

241,288

ZFIN Antibody Expression Assay Records

Show

902 KB

7,298

ZFIN Genes with Expression Assay Records

Show

9 MB

73,562

Genetic Marker Relationships

Show

9 MB

94,230

Genetic Markers

Genetic Marker

Show

9 MB

147,520

Previous ZFIN IDs
(includes former and current ZFIN IDs for merged data)

Show

1 MB

33,135

SNP Data

Show

133 MB

2,346,619

Genomic Feature Data

All Genomic Features

Show

4 MB

39,352

Construct Components

Show

992 KB

7,012

Genomic Features and their affected genes
(alleles, deficiencies, translocations)

Show

2 MB

25,059

Transgenic Insertions

Show

2 MB

26,837

Genotype Data

Genotype Backgrounds

Show

434 KB

7,306

Genotype Features

Show

3 MB

20,904

1	2	3	4	5	6	7	8	9	10	11	12	13
Genotype ID	Genotype Name	Genotye Unique Name	Allele ID	Allele Name	Allele Abbreviation	Allele Type	Allele Display Type	Gene or Construct Symbol	Corresponding ZFIN Gene ID/Construct ID	Allele Zygosity	Construct Name	Construct ZdbId

Genotype Features (removed or displaced genes)

Show

18 KB

199

Genotype-Publication relation

Show

1 MB

33,449

Image Data

Image-Figure translations
Note: Images are not provided due to copyright restrictions

Show

4 MB

88,814

Knockdown Reagent Data

CRISPR

Show

3 KB

Morpholino

Show

978 KB

6,515

TALEN

Show

23 KB

169

Mapping Data

Mapping Data from the 6 Zebrafish Mapping Panels

Show

1 MB

26,654

Orthology Data

Drosophila and Zebrafish Orthology

Show

4 KB

Human and Zebrafish Orthology

Show

1 MB

14,835

Mouse and Zebrafish Orthology

Show

1 MB

12,073

Phenotypic Zebrafish genes with Human Orthology

Show

109 KB

2,564

Phenotype Data

Genotype-Figure relation

Show

768 KB

20,880

Genotypes with Phenotypes

Show

17 MB

77,990

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23
Genotype ID	Genotype Name	Start Stage ID	Start Stage Name	End Stage ID	End Stage Name	Affected Structure or Process 1 subterm ID	Affected Structure or Process 1 subterm Name	Post-composed Relationship ID	Post-composed Relationship Name	Affected Structure or Process 1 superterm ID	Affected Structure or Process 1 superterm Name	Phenotype Keyword ID	Phenotype Keyword Name	Phenotype Tag	Affected Structure or Process 2 subterm ID	Affected Structure or Process 2 subterm name	Post-composed Relationship (rel) ID	Post-composed Relationship (rel) Name	Affected Structure or Process 2 superterm ID	Affected Structure or Process 2 superterm name	Publication ID	Environment ID

Genotypes with Phenotypes (obo format)

Show

11 MB

80,526

1	2	3	4	5	6	7	8	9	10	11	12
Genotype ID	Genotype Name	Start Stage OBO ID	End Stage OBO ID	Affected Structure or Process 1 superterm OBO ID	Affected Structure or Process 1 subterm OBO ID	Phenotype Keyword OBO ID	Phenotypep Modifier	Affected Structure or Process 2 superterm OBO ID	Affected Structure or Process 2 subterm OBO ID	Publication ID	Environment ID

Phenotype Environment Description

Show

548 KB

9,052

Phenotype for Zebrafish genes with fin phenotype

Show

242 KB

970

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26
#	Gene Symbol	Gene ID	Affected Structure or Process 1 subterm OBO ID	Affected Structure or Process 1 subterm name	Post-Composed Relationship ID	Post-Composed Relationship Name	Affected Structure or Process 1 superterm OBO ID	Affected Structure or Process 1 superterm name	Phenotype Keyword OBO ID	Phenotype Quality	Phenotype Tag	Affected Structure or Process 2 subterm OBO ID	Affected Structure or Process 2 subterm name	Post-Composed Relationship ID	Post-Composed Relationship Name	Affected Structure or Process 2 superterm OBO ID	Affected Structure or Process 2 superterm name	Genotype ID	Genotype Name	Knockdown Reagent ID	Stage Start	Stage End	Genotype Experiment ID	Publication ID	Figure ID

Phenotype for Zebrafish genes with Human Orthology

Show

3 MB

34,592

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19
Gene ID	Entrez Zebrafish Gene ID	Entrez Human Gene ID	ZFIN Gene Symbol	Affected Structure or Process 1 subterm OBO ID	Affected Structure or Process 1 subterm name	Post-Composed Relationship ID	Post-Composed Relationship Name	Affected Structure or Process 1 superterm OBO ID	Affected Structure or Process 1 superterm name	Phenotype Keyword OBO ID	Phenotype Quality	Phenotype Tag	Affected Structure or Process 2 subterm OBO ID	Affected Structure or Process 2 subterm name	Post-Composed Relationship ID	Post-Composed Relationship Name	Affected Structure or Process 2 superterm OBO ID	Affected Structure or Process 2 superterm name

Phenotype of Zebrafish Genes

Show

15 MB

64,000

1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	21	22	23	24	25	26
ID	Gene Symbol	Gene ID	Affected Structure or Process 1 subterm ID	Affected Structure or Process 1 subterm Name	Post-composed Relationship ID	Post-composed Relationship Name	Affected Structure or Process 1 superterm ID	Affected Structure or Process 1 superterm Name	Phenotype Keyword ID	Phenotype Keyword Name	Phenotype Tag	Affected Structure or Process 2 subterm ID	Affected Structure or Process 2 subterm name	Post-composed Relationship (rel) ID	Post-composed Relationship (rel) Name	Affected Structure or Process 2 superterm ID	Affected Structure or Process 2 superterm name	Genotype ID	Genotype Display Name	Knockdown Reagent ID	Start Stage ID	End Stage ID	Genotype Environment ID	Publication ID	Figure ID

Previous Names

Show

8 MB

124,391

Publications

ZFIN Bibliography

Show

3 MB

15,636

ZFIN Marker IDs / UniProtKB IDs to ZFIN Pub IDs & PubMed IDs

Show

4 MB

62,865

ZFIN Publication IDs: ZFIN IDs to PubMed IDs

Show

517 KB

19,642

Sequence Coordinates

Assembly: Ensembl

Show

166 MB

1,049,576

Complete Assembly Clones: Ensembl

Show

3 MB

33,167

Transgenic Insertion: ENSEMBL

Show

2 MB

15,223

ZFIN Genes with Antibodies: Ensembl

Show

58 KB

544

ZFIN Genes with Expression: Ensembl

Show

1 MB

9,511

ZFIN Genes with Phenotype: Ensembl

Show

249 KB

2,300

ZFIN Genes: Ensembl

Show

3 MB

20,953

ZFIN Morpholinos: Ensembl

Show

530 KB

4,530

Sequence Data

Transcripts

Show

4 MB

48,358

ZFIN Gene IDs indirectly and directly associated with Sequence Accessions via cDNA & EST

Show

4 MB

92,825

ZFIN Gene IDs indirectly associated with Sequence Accessions via cDNA & EST

Show

1 MB

41,501

ZFIN Marker associations to Ensembl IDs
(Only associations with 1:1 relationships between ZFIN marker IDs and Ensembl IDs are stored in ZFIN. All associations can be obtained using BioMart http://www.ensembl.org/biomart/martview)

Show

1 MB

19,196

ZFIN Marker associations to GenBank sequence data

Show

5 MB

119,149

ZFIN Marker associations to GenPept protein data

Show

2 MB

44,662

ZFIN Marker associations to InterPro protein data

Show

117 MB

2,479,111

ZFIN Marker associations to NCBI Gene data

Show

969 KB

20,919

ZFIN Marker associations to RefSeq sequence data

Show

2 MB

60,561

ZFIN Marker associations to Sanger Vega data

Show

2 MB

30,610

ZFIN Marker associations to UniGene sequence data

Show

909 KB

20,217

ZFIN Marker associations to UniProt protein data

Show

2 MB

47,332

Wildtype Lines

Show

1006 bytes

ZFIN Identifiers

Show

18 MB

215,960

Externally Hosted Files:

The 'File Name'-links point to the latest version. To obtain previous versions you have to check the archive of the external source.