ensembl release 34

Hi,

How to get gene description, entrez ID and GO information, etc for ensembl release-34?

ftp.ensemblgenomes.org/pub/release-34/plants/tsv/zea_mays/

Zm00001d027267 Zm00001d027268

using Biomart I am getting empty result for all these headers such gene description etc.

gene ensembl genomes

• 1,943 views • link

updated 9.5 years ago by Emily

• written 9.5 years ago by manoharankumar01 •

You seem to have the wrong link for FTP. Try this: ftp://ftp.ensemblgenomes.org/pub/plants/release-34/fasta/zea_mays/

• 0 views • link

written 9.5 years ago by GenoMax

Can you tell us the filters and attributes you're using in BioMart, please? I filtered by the two IDs you listed and got the attributes you said and I got this.

• 0 views • link

written 9.5 years ago by Emily

Thanks I was using filter uniprortKB.

But now for this version protein coding gene description seems to be only 1560.

Compare to previous version release 31 has 28568 protein coding gene description.

Is there a way to get protein coding gene description similar to previous version?

If not can you suggest a way to map release 34 gene IDs to release 31 gene IDs?

• 0 views • link

written 9.5 years ago by manoharankumar01 •

0 answers

No answers yet.

More posts like this

GO annotation with entrez gene id for non-model organism
written 6.4 years ago by bifStudent •

Hi everybody, I am working on a shiny project which supports users lacking programming skills to perform GO enrichment analysis. Unfortunately I am struggling to …
Safe to convert entrez gene id to ensembl gene id
written 6.5 years ago by tmms •

Hello I have performed a differential expression analysis with DESeq2 in R. I obtained a list of differentially expressed genes. These genes are identified by …
biomaRt getBM function report some NA
written 7.4 years ago by Bastien Hervé

I'm trying to get some `entrez` ids from some gene names using [biomaRt][1] In my example below I have 2 genes `Igha` and `Mlc1` for …
Ensembl ID found on the site but not in downloaded flat file
written 7.4 years ago by Chat-ra •

Hello everyone! I’ve downloaded several Ensembl file (the entrez and uniprot ones) found here: http://ftp.ensembl.org/pub/release-95/tsv/homo_sapiens/ While working I’ve encountered an issue. Some of the Ensembl …
Does ensembl biomart provide ortholog information incomplete?
written 7.7 years ago by Yingzi Zhang

Deal all, I exported human-pig ortholog relationship information from ensembl biomart. For gene SIRPA, it showed empty information of pig gene/transcrip/protein id nor any ortholog …
Reference genome for wheat/ Triticum aestivum
written 8.7 years ago by ammarsabir15

I want to work on wheat genomics, for doing this I am not sure where to get the reference sequence for wheat because if you …
BioMart up-to-date with NCBI ?
written 11.3 years ago by lindfors.erno •

Hi all, I want to convert mouse (MGI) gene symbols to entrez gene ids by using [BioMart's R interface][1]. I every now and then come …
Biomart R package - help writing biomart results into existing file.
written 12.0 years ago by jsgorams •

Just starting to learn R so bear with me. We've conducted an RNA-seq experiment and are working on getting gene ontology information on the sequenced …
Is The Biomart Registry Accessed Via The Bioconductor Package Out Of Date?
written 13.3 years ago by Georg Summer

I am in the process of updating some annotations using the Ensembl Biomart. Using the biomaRt package in R I do the following: mart = …
Different Results With Goose And Biomart
written 13.4 years ago by TitoPullo

<p>I'm using the biomaRt package for R in order to get all the GO terms associated with with a particular Gene ID (Entrez ID). The …