Output File Format


This page provides information about the format of the output file supplied by the GeneALaCart Batch Queries engine of GeneCards.

General Comments


Field formats

GeneCards_ID

gc_id

Category

protein-coding, pseudogene, RNA gene, genetic locus, gene cluster, or uncategorized

Gene Description

Gene description according to HGNC or Entrez Gene

Approval

Approved, not approved according to HGNC

Source

Gene symbol from HGNC, Entrez Gene or Ensembl

GIFtS

An integer that represents the GeneCards Inferred Functionality Score

Aliases and Descriptions

alias1 or description1|alias2 or description2|alias3 or description3|...

External IDs

entrezgene_id|ensembl_id|hgnc_id|

EntrezGene summary

Summary from EntrezGene

UniProtKB/Swiss-Prot summary

Function1|Function2|Function3|...

Tocris summary

Summary from Tocris

SABiosciences Regulatory transcription factor binding sites(tfbs)

Tfbs1|Tfbs2|Tfbs3|....

Chromosome

1-22 or X,Y,MT (mitochondria). NA appears where chromosome is unknown.

Strand

Plus, Minus or NA (where strand is unknown)

Cytogenetic band

Cytogenetic band according to Entrez Gene, Ensembl and/or HGNC

Gene start

Chromosomal coordinate in bp from pter

Gene end

Chromosomal coordinate in bp from pter

Gene size

Size of genomic sequence in bp

Contig

For genes that don't have a chromosomal location

UniProtKB Protein details

source:aliases|uniprotkb protein_id1#uniprotkb secondary accessions1#protein name#size#cofactor & cofactor#subunit & subunit#subcellular location & subcellular location#tissue specificity & tissue specificity#developmental stage & developmental stage#ptm & ptm#miscellaneous & miscellaneous|
uniprotkb protein_id2#uniprotkb secondary accessions2#protein name#size#cofactor..#subunit..#subcellular location..#tissue specificity..#developmental stage..#ptm..#miscellaneous..|
uniprotkb protein_id3#uniprotkb secondary accessions3#protein name#size#cofactor..#subunit..#subcellular location..#tissue specificity..#developmental stage..#ptm..#miscellaneous..|...

RefSeq Protein ID

refseq protein_id1|refseq protein_id2|refseq protein_id3|...

Ensembl Protein ID

ensembl protein_id1|ensembl protein_id2|ensembl protein_id3|...

HGNC families

family_name1:description|family_name2:description|family_name3:description|...

IUPHAR families

family1#family2#family3...

InterPro domains and families

InterPro_id1#domain_name|InterPro_id2#domain_name...

UniProtKB Domains and Families

source:uniprotkb_id1#domain & domain..#similarity & similarity..|uniprotkb_id2#domain & domain..#similarity & similarity..|uniprotkb_id3#domain & domain..#similarity & similarity..|...

Function - UniProtKB

source:uniprotkb_id1#function|uniprotkb_id2#function|uniprotkb_id3#function...

Function - MGI mutant phenotype

Allele1: MGI_id1#Phenotypes: |Allele2: MGI_id2#Phenotypes: phenotype_id1#phenotype_name||phenotype_id2#phenotype_name...

Function - SABiosciences bound target genes

gene1|gene2|gene3|...

Function - QIAGEN regulating microRNAs

microRNA_id1|microRNA_id2|microRNA_id3|...

Gene Ontologies (GO)

go_id1#go_term1|go_id2#go_term2|go_id3#go_term3|...

Pathways (EMD Millipore)

emd millipore_id1#emd millipore_pathway1|emd millipore_id2#emd millipore_pathway2|emd millipore_id3#emd millipore_pathway3|...

Pathways (R&D Systems)

r&d systems_pathway1|r&d systems_pathway2|r&d systems_pathway3|...

Pathways (QIAGEN)

qiagen_pathway1|qiagen_pathway2|qiagen_pathway3|...

Pathways (CST)

cst_id1#cst_pathway1|cst_id2#cst_pathway2|cst_id3#cst_pathway3|...

Pathways (Tocris)

tocris_id1#tocris_pathway1|tocris_id2#tocris_pathway2|tocris_id3#tocris_pathway3|...

Pathways (Thomson Reuters)

thomson reuters_id1#thomson reuters_pathway1|thomson reuters_id2#thomson reuters_pathway2|thomson reuters_id3#thomson reuters_pathway3|...

Pathways (BioSystems)

biosystems_pathway1|biosystems_pathway2|biosystems_pathway3|...

Pathways (Reactome)

reactome_id1#reactome_pathway1|reactome_id2#reactome_pathway2|reactome_id3#reactome_pathway3|...

Pathways (PharmGKB)

pharmgkb_pathway1|pharmgkb_pathway2|pharmgkb_pathway3|...

Pathways (KEGG)

kegg_id1#kegg_pathway1|kegg_id2#kegg_pathway2|kegg_id3#kegg_pathway3|...

Interactions (UniProtKB)

interactant1#external_id1#interaction_id,interaction_id|interactant2#external_id2#interaction_id,interaction_id|interactant3#external_id3#interaction_id, interaction_id|...

Interactions (MINT)

external_id1#interaction_id,interaction_id|external_id2#interaction_id,interaction_id|external_id3#interaction_id, interaction_id|...

Interactions (STRING)

interactant1#external_id1#experiments_score#databases_score|interactant2#external_id2#experiments_score#databases_score|interactant3#external_id3#experiments_score#databases_score|...

Interactions (I2D)

interactant1#score|interactant2#score|interactant3#score|...

Tocris Compounds

compound1#action#CAS number|compound2#action#CAS number|compound3#action#CAS number|...

HMDB Compounds

compound1#synonyms#CAS number#pubmed_ids|compound2#synonyms#CAS number#pubmed_ids|compound3#synonyms#CAS number#pubmed_ids|...

DrugBank Compounds

compound1#synonyms#CAS number#type#actions#pubmed_ids|compound2#synonyms#CAS number#type#actions#pubmed_ids|compound3#synonyms#CAS number#type#actions#pubmed_ids|...

IUPHAR Ligands

ligand1#type#action#affinity#pubmed_ids|ligand2#type#action#affinity#pubmed_ids|ligand3#type#action#affinity#pubmed_ids|...

Novoseek Compounds

compound1|compound2|compound3|...

PharmGKB Compounds

compound1#relations#pubmed_ids|compound2#relations#pubmed_ids|compound3#relations#pubmed_ids|...

Transcripts (Refseq)

transcript1|transcript2|transcript3|...

Transcripts (Unigene)

ug_cluster1#description|ug_cluster2#description|ug_cluster3#description...

Transcripts (Ensembl)

transcript1|transcript2|transcript3|...

Orthologs

source:organism1#taxonomic classification#gene1#percent protein similarity#percent nucleotide similarity#entrezgene_id#genbank_id#protein_id|organism2#taxonomic classification#gene2#percent protein similarity#percent nucleotide similarity#entrezgene_id#genbank_id#protein_id|organism3#taxonomic classification#gene3#percent protein similarity#percent nucleotide similarity#entrezgene_id#genbank_id#protein_id|...

The organisms are depicted by their two or three letter acronyms as follows:

AcronymScientific nameCommon name
AcAnolis carolinensisLizard
AgaAnopheles gambiaeAfrican malaria mosquito
AmApis melliferaHoney bee
AnAspergillus nidulansFilamentous fungus
AtArabidopsis thalianaThale cress
BtBos taurusCow
CelCaenorhabditis elegansWorm
CfaCanis familiarisDog
CinCiona intestinalisSea squirt
CreChlamydomonas reinhardtiiGreen algae
CsCiona savignyiSea squirt
DdiDictyostelium discoideumAmoeba
DmDrosophila melanogasterFruit fly
DrDanio rerioZebrafish
EcEscherichia coliE. coli
EgAshbya gossypiiA. gosspyii yeast
GgaGallus gallusChicken
GmaGlycine maxSoybean
HvHordeum vulgareBarley
KlKluyveromyces lactisK. lactis yeast
LesLycopersicon esculentumTomato
MdMonodelphis domesticaOppossum
MgrMagnaporthe griseaRice blast fungus
MmMus musculusMouse
MtMycobacterium tuberculosisActinobacteria
MtrMedicago truncatulaMedicago trunc
NcrNeurospora crassaBread mold
NmNeisseria meningitidisBeta proteobacteria
NvNematostella vectensisSea anemone
OmyOncorhynchus mykissRainbow trout
OaOrnithorhynchus anatinusPlatypus
OsOryza sativaRice
PfPlasmodium falciparumMalaria parasite
PgPuccinia graminisStem rust fungus
PhPyrococcus horikoshiiArchea
PiPhytophthora infestansChromalveolata
PpPongo pygmaeusOrangutan
PpaPhyscomitrella patensMoss
PtPan troglodytesChimpanzee
PtaPinus taedaLoblolly pine
RnRattus norvegicusRat
SbiSorghum bicolorSorghum
ScSaccharomyces cerevisiaeBaker's yeast
SmaSchistosoma mansoniSchistosome parasite
SofSaccharum officinarumSugarcane
SpSchizosaccharomyces pombeFission yeast
SpnStreptococcus pneumoniaeFirmicute bacteria
SpuStrongylocentrotus purpuratusSea urchin
SscSus scrofaPig
StrXenopus tropicalisTropical clawed frog
TaTriticum aestivumWheat
TadTrichoplax adhaerensTrichoplax
TgoToxoplasma gondiiToxoplasmosis
VvaVitis viniferaAlicante grape
WpWolbachia pipientisAlpha proteobacteria
XlXenopus laevisAfrican clawed frog
ZmZea maysCorn


Ensembl pan Orthologs

source:organism1#taxonomic classification#gene1#percent amino acid similarity#orthology type|organism2#taxonomic classification#gene2#percent amino acid similarity#orthology type|organism3#taxonomic classification#gene3#percent amino acid similarity#orthology type|...

Homologene Paralogs

gene1|gene2|gene3|...

Ensembl Paralogs

gene1|gene2|gene3|...

Genomic Variants (NCBI)

number of snps: ncbi_id1#location type#minor allele frequency#sample size#populations studied#validation#position#nucleotide change#amino acid change#sequence#number of sources|ncbi_id2#location type#minor allele frequency#sample size#populations studied#validation#position#nucleotide change#amino acid change#sequence#number of sources...

Genomic Variants (SABiosciences Cancer Mutation PCR Arrays)

sabiosciences_id1#sabiosciences_cancer_array1|sabiosciences_id2#sabiosciences_cancer_array2|sabiosciences_id3#sabiosciences_cancer_array3...

OMIM Disorders

omim_id#disorder_id1|disorder_id2|disorder_id3|...

MalaCards Disorders

disorder1|disorder2|disorder3|...

UniProtKB Disorders

source:uniprotkb_id1#disorder & disorder..|uniprotkb_id2#disorder & disorder..|uniprotkb_id3#disorder & disorder..|...

Novoseek Disorders

disorder1|disorder2|disorder3|...

DISEASES Disorders

disorder1|disorder2|disorder3|...

Publications

pubmed_id1|pubmed_id2|pubmed_id3|...






Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

Version: 3.12.258 10 Dec 2014
hostname: 356980-web2.xennexinc.com index build: 128 solr: 1.4