EMBL-EBI at Plant and Animal Genome conference

PAG-ASIA Singapore13th July 2015

Genomic Resources at the EMBL-EBI

Denise Carvalho-Silva (Ensembl and Ensembl Genomes)Gary Saunders (European Variation Archive, EVA)

www.ebi.ac.uk@emblebi

What is EMBL-EBI?•  Part of the European Molecular

Biology Laboratory•  European Bioinformatics Laboratory•  Based in Hinxton - Cambridge (UK)

EMBL-EBI staff:> 500 people> 50 nations

Europe’s hub for:Bioinformatics Services (free)User Training Computational ResearchEngagement with the Industry

EMBL-EBI users: a one-day snapshotHub in Europe à worldwide user community

www.ebi.ac.uk

5

www.ebi.ac.uk/services

Our services

Archive

ClassifyShareAnalyse

Provide tools

EMBL-EBI’s data cycle

This workshop: 1:00-3:00 pm

www.ebi.ac.uk/training

@EBItraining

Training at EMBL-EBI, off-site and online

Register to EMBL-EBI train online•  www.ebi.ac.uk/training/online

•  Take – record quizzes•  Get updates on new courses, features

Quarterly newsletter

•  Get involved in usability testing

PAG-ASIA Singapore13th July 2015

Ensembl and Ensembl Genomes: Browser and toolkit

Denise Carvalho-Silva, PhD

www.ensembl.orgwww.ensemblgenomes.org

@ensembl@ensemblgenomes

EBI is an Outstation of the European Molecular Biology Laboratory.

Outline

•  Introduction to Ensembl and Ensembl Genomes

•  Some highlights of last year

•  Live demos1.  Browser and custom data upload2.  Toolkit: BioMart and VEP

•  How to cite and connect with us


Outline






Do We Need Genome Browsers?q YES q NO



Annotation: Making sense


The Ensembl projects

www.ensembl.org

www.ensemblgenomes.org

•  launched in 1999

•  Ensembl gene annotation•  EBI and WTSI

•  launched in 2009

•  community gene annotation•  EBI


Vertebrate genomes

ww

w.e

nsem

bl.o

rg

pre.

ense

mbl

.org

>80 genomes* D. melanogaster

C. elegans S. cerevisae

*Release 80 May 2015


Extends the use of Ensembl to other speciesWider taxonomic range (v27, >25K genomes)

Non-vertebrate genomes

x 53x 39x 408x 133x 24,913

plants.ensembl.org


Dicotyledons

12 in 7 orders: Brassicales, Fabales, Malpighiales, Malvales, Rosales, Solanales, Vitales


Monocotyledons

Poales

Zingiberales

21 in 2 ordersetc…


'Others': 6 in 5 Classes


Comparative GenomicsGene models

Custom data display

Programmatic access Free code and data

RegulationVariation Toolkit

Ensembl features

How to access our data

�� !�� "��# ��$� � %&�� &��!�� "��$� ��' ��(�� )�� "��*��+� ��%��$,-�,��.��/��%� ��0�122�3-4,556�272829

��!��!"�%�� "��

��

��

��

��

�� !�" #� �� $$� ��

%��

&�� !�� '�$� ��()**�� "�#�� ++��

&�� $$��%�&��)+�"))��

%��

��

��,�� ,�� &�� -%��

��.��/��0��

�� %�� '��$� �� 1�� ,�� %�� /��0��$��(�'��

�� ) �� ,�� 2� �� 3� ��*�� +�(�� ,��

/�� %�� ,� ��$��,� ��-�� -�� '�� !�� 0�� %�� +� �� $��4��5��4��5��6�62��4��5�� 4��5� �� 4��5� �� ,��

��%��

��,�� %��

��/��(��

�� 7�� 8�� 7�� .�� /�� -��-�� 012�3/��

%�� 7�� '�� -�-�$�� ,�� $��'�� /��$��(�0��$ �� -�� %��

��%��/��9��3�� 9��

�� %�� /�� $�� 04�� ,��4��,��5��4��01��2��,�� ,�� 5�-��

��!$�+�!�� :�� (�61�7��%��;��3��$��3��0��/��3��/8�!��/��-��9��

� !�� % !�� D�( #&�E�$� �� !��

1��

%��4�0��//0�� %.6�<%� �� ,�� 7��$� �� :�� 0�� ,��

<��

�� '�� -��$$�$� �-�� 4�� 5�� 4��0��0� ,�0��4��0�� 5� �� :��

&�� :��%0��

!�� : ��&� '��%� '� �� 3%��-7;7-9��-79-;,4�<�� '��%�' ��"��'��"� :�� " ��'� �� *��)�� (�� 3,�52��-658;9� �� ,�-,*�-=2-=94�� $$�� 3$$>(-5;;-8>,��$$>(-5;68->,��$$>/--7;52>,4��!�� "��# ��$� � %&�� &��"��'��0�?��%�� '��%�'� ��!�� "��.�� @�� < �� %��3 �=>5--=A5-,64��%��%��B�595;,-�A�$�.!��(��?C� ?� �� "" �� &� �� !�� "�� <�� < �� %�� =� ��"�� "��'�� %�� )�� D%�� 6,56-,� 3*��+�� A� �� 4?C� �� %�� "" �� "��'��0� ?�� %� � � �� '��%� '� �� !�� "�� &@�� < �� %�� 3 �=>5--=A5-,64� �� %�� %�� B�*!D��*A 2A5-,-A52,;-2�3!.�D��D��4?


Outline






Highlights•  New assemblies

•  Genotype data for Iranian and Moroccan sheep*

•  Update SNP and phenotype data

http://appris.bioinfo.cnio.es

*http://projects.ensembl.org/nextgen/#fn1

http://www.ebi.ac.uk/gxa/home

•  APPRIS

• 


Highlights


Highlights


•  New assemblies

Highlights

•  New RNA-Seq data

•  New whole genome alignments

•  Toolkit: assembly converter v2.4 v25

•  New variation data


Outline






Live demos

1.  Browsers

•  Viewing our annotation

•  Attaching custom data

2.  Toolkit

1. 

2.  v

The Arabidopsis floral homeotic gene APETALA1 (AP1) encodes a putative TF that acts locally to specify the identity of the floral meristem and to determine sepal and petal development (https://www.wikigenes.org/e/gene/e/843244.html).

Browser demo


Toolkit: BioMart•  Data export tool for easy retrieval of Ensembl/Ensembl Plants data

DATA FILTERS ATTRIBUTES RESULTS

e.g. Gene IDs

e.g. TablesFASTAwheate.g. Gene

e.g. HomologsSequencesDomains


Live demo: exporting data with BioMart

I’ve got a list of affymetrix probeset IDs from my microarray experiment that seem to map uniquely to genes in the chicken genome. Here they are: Gga.1444.1.S1_at, Gga.12669.1.S1_at, GgaAffx.7784.1.S1_at, GgaAffx.12530.1.S1_at

•  What are the Ensembl IDs, names and locations of these genes

•  Possible function according to the Gene Ontology (GO) names

•  Export their protein sequences and get them emailed to me

Tip: include probeset IDsin the results table

Toolkit: The Variant Effect Predictor

•  Annotate your own SNPs and CNVs

•  Different input formats

•  SIFT/PolyPhen for missense variantsPMID: 20562413

Perl script Web interface REST API

XML


CODINGSynonymous

INTRONIC5’ UTR

ATG AAAAAAARegulatory

Splice sites

CODINGMissense

3’ UTR 5’ Upstream 3’ downstream

Mapping variants on transcripts

Identify transcripts that overlap variants and predict their functional consequence using


Live demo: annotating my variants

My GWAS experiments in pigs have identified few variants associated with meat quality:chr 18, genomic coordinate 37452309, alleles A/T, forward strandchr 10, genomic coordinate 17387779, alleles G/A, forward strandchr X, genomic coordinate 120285089, alleles A/-, forward strand

Can I use VEP to annotate them and find out:•  in which genes and transcripts they map to•  what effect do these variants have on these transcripts?•  are these variants known in public databases?


Ensembl videos


Outline





Latest publication


Latest Publication

Acknowledgements

Funding European Commission Framework Programme 7


Acknowledgements

Our users and our funders

Ensembl Genome team


? ??

? ?

? ?

? ? ?

PAG

PAG

Connect with us

[email protected]

[email protected]

Ensembl workshops at your institute

ActivitiesCountriesContinentsTrainersParticipants

~10019

3~30

2,087

Host our workshops! [email protected]

2014

Science

EMBL-EBI at Plant and Animal Genome conference