Download Archive: 2014.04.17

ZFIN Data Reports from: 17 Apr 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

205 KB

2,873

Zebrafish Anatomy Term Relationships

Show

169 KB

5,428

Zebrafish Anatomy Term Synonyms

Show

139 KB

2,646

Zebrafish Development Stage Terms

Show

315 KB

13,380

Zebrafish Stage Series

Show

2 KB

Antibody Data

Antibodies

Show

119 KB

1,496

Antibody Expressions in wild-type

Show

259 KB

4,663

Fish

Fish Components

Show

10 MB

61,834

Gene Expression

Expression data for wildtype fish

Show

24 MB

153,924

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

547 KB

8,609

Expression Experiment-Figure

Show

14 MB

253,539

Zebrafish Gene Expression by Stage and Anatomy Term

Show

22 MB

245,024

ZFIN Antibody Expression Assay Records

Show

916 KB

7,413

ZFIN Genes with Expression Assay Records

Show

9 MB

74,872

Genetic Marker Relationships

Show

9 MB

94,408

Genetic Markers

Genetic Marker

Show

9 MB

147,694

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

Show

1 MB

33,152

SNP Data

Show

133 MB

2,346,457

Genomic Feature Data

All Genomic Features

Show

4 MB

39,400

Construct Components

Show

1019 KB

7,210

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

Show

2 MB

25,074

Transgenic Insertions

Show

2 MB

26,872

Genotype Data

Genotype Backgrounds

Show

435 KB

7,324

Genotype Features

Show

3 MB

21,127

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

33,697

Image Data

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

Show

4 MB

89,533

Knockdown Reagent Data

CRISPR

Show

3 KB

Morpholino

Show

995 KB

6,628

TALEN

Show

23 KB

172

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

14,985

Mouse and Zebrafish Orthology

Show

1 MB

12,254

Phenotypic Zebrafish genes with Human Orthology

Show

111 KB

2,611

Phenotype Data

Genotype-Figure relation

Show

782 KB

21,256

Genotypes with Phenotypes

Show

17 MB

79,412

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

12 MB

82,012

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

568 KB

9,383

Phenotype for Zebrafish genes with fin phenotype

Show

245 KB

979

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

35,389

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

65,010

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

125,045

Publications

ZFIN Bibliography

Show

3 MB

15,807

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

Show

4 MB

64,559

ZFIN Publication IDs: ZFIN IDs to PubMed IDs

Show

522 KB

19,845

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

59 KB

555

ZFIN Genes with Expression: Ensembl

Show

1 MB

9,537

ZFIN Genes with Phenotype: Ensembl

Show

253 KB

2,339

ZFIN Genes: Ensembl

Show

3 MB

20,952

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

92,988

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

119,270

ZFIN Marker associations to GenPept protein data

Show

2 MB

44,668

ZFIN Marker associations to InterPro protein data

Show

118 MB

2,505,048

ZFIN Marker associations to NCBI Gene data

Show

970 KB

20,944

ZFIN Marker associations to RefSeq sequence data

Show

2 MB

60,649

ZFIN Marker associations to Sanger Vega data

Show

2 MB

30,610

ZFIN Marker associations to UniGene sequence data

Show

909 KB

20,239

ZFIN Marker associations to UniProt protein data

Show

2 MB

48,151

Wildtype Lines

Show

1006 bytes

ZFIN Identifiers

Show

18 MB

216,516

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.