Download Archive: 2014.07.21

ZFIN Data Reports from: 21 Jul 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

206 KB

2,884

Zebrafish Anatomy Term Relationships

Show

170 KB

5,456

Zebrafish Anatomy Term Synonyms

Show

140 KB

2,661

Zebrafish Development Stage Terms

Show

315 KB

13,380

Zebrafish Stage Series

Show

2 KB

Antibody Data

Antibodies

Show

127 KB

1,594

Antibody Expressions in wild-type

Show

274 KB

4,918

Fish

Fish Components

Show

10 MB

63,175

Gene Expression

Expression data for wildtype fish

Show

25 MB

157,217

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

571 KB

9,005

Expression Experiment-Figure

Show

15 MB

262,714

Zebrafish Gene Expression by Stage and Anatomy Term

Show

23 MB

253,801

ZFIN Antibody Expression Assay Records

Show

999 KB

8,101

ZFIN Genes with Expression Assay Records

Show

9 MB

77,429

Genetic Marker Relationships

Show

9 MB

94,784

Genetic Markers

Genetic Marker

Show

9 MB

148,160

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

Show

1 MB

33,181

SNP Data

Show

133 MB

2,344,750

Genomic Feature Data

All Genomic Features

Show

4 MB

39,630

Construct Components

Show

1 MB

8,177

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

Show

2 MB

25,107

Transgenic Insertions

Show

2 MB

27,075

Genotype Data

Genotype Backgrounds

Show

437 KB

7,372

Genotype Features

Show

3 MB

21,843

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

20 KB

214

Genotype-Publication relation

Show

1 MB

34,507

Image Data

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

Show

4 MB

90,816

Knockdown Reagent Data

CRISPR

Show

5 KB

Morpholino

Show

1 MB

6,826

TALEN

Show

24 KB

178

Mapping Data

Mapping Data from the 6 Zebrafish Mapping Panels

Show

1 MB

26,654

Orthology Data

Drosophila and Zebrafish Orthology

Show

5 KB

Human and Zebrafish Orthology

Show

1 MB

15,183

Mouse and Zebrafish Orthology

Show

1 MB

12,486

Phenotypic Zebrafish genes with Human Orthology

Show

114 KB

2,682

Phenotype Data

Genotype-Figure relation

Show

809 KB

22,024

Genotypes with Phenotypes

Show

12 MB

85,061

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	Phenotype Modifier	Affected Structure or Process 2 superterm OBO ID	Affected Structure or Process 2 subterm OBO ID	Publication ID	Environment ID

Genotypes with Phenotypes

Show

18 MB

82,301

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

Phenotype Environment Description

Show

598 KB

9,884

Phenotype for Zebrafish genes with fin phenotype

Show

258 KB

1,031

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

4 MB

36,728

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

16 MB

67,067

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

9 MB

131,284

Publications

ZFIN Bibliography

Show

3 MB

16,754

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

Show

4 MB

65,765

ZFIN Publication IDs: ZFIN IDs to PubMed IDs

Show

550 KB

20,870

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

61 KB

572

ZFIN Genes with Expression: Ensembl

Show

1 MB

9,685

ZFIN Genes with Phenotype: Ensembl

Show

261 KB

2,418

ZFIN Genes: Ensembl

Show

3 MB

21,392

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

93,974

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

Show

1 MB

41,497

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

19,704

ZFIN Marker associations to GenBank sequence data

Show

5 MB

119,748

ZFIN Marker associations to GenPept protein data

Show

2 MB

44,651

ZFIN Marker associations to InterPro protein data

Show

128 MB

2,692,453

ZFIN Marker associations to NCBI Gene data

Show

994 KB

21,423

ZFIN Marker associations to RefSeq sequence data

Show

3 MB

62,174

ZFIN Marker associations to Sanger Vega data

Show

2 MB

35,114

ZFIN Marker associations to UniGene sequence data

Show

918 KB

20,438

ZFIN Marker associations to UniProt protein data

Show

2 MB

49,388

Wildtype Lines

Show

1006 bytes

ZFIN Identifiers

Show

18 MB

217,588

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.