DESIGNING TRAINING REGULATORY DATASETS Enrique Blanco Xavier Messeguer Roderic Guigó

DESIGNING TRAINING DESIGNING TRAINING REGULATORY DATASETSREGULATORY DATASETS

Enrique BlancoXavier Messeguer

Roderic Guigó

OUR APPROACHOUR APPROACH

Enrique Blanco [http://genome.imim.es] - RegCreative Jamboree 2006

1. SEQUENCE AND FUNCTION

SIMILARSEQUENCE

SIMILAR FUNCTION

Transthyretin NP_000362 (human) - NP_036813 (rat):

MASHRLLLLCLAGLVFVSEAGPTGTGESKCPLMVKVLDAVRGSPAINVAVMASLRLFLLCLAGLIFASEAGPGGAGESKCPLMVKVLDAVRGSPAVDVAV*** **:*******:*.***** *:********************::***

HVFRKAADDTWEPFASGKTSESGELHGLTTEEEFVEGIYKVEIDTKSYWKKVFKRTADGSWEPFASGKTAESGELHGLTTDEKFTEGVYRVELDTKSYWK:**:::**.:*********:**********:*:*.**:*:**:*******

ALGISPFHEHAEVVFTANDSGPRRYTIAALLSPYSYSTTAVVTNPKEALGISPFHEYAEVVFTANDSGHRHYTIAALLSPYSYSTTAVVSNPQN*********:*********** *:******************:**::


2. FUNCTION AND SEQUENCE

SIMILARSEQUENCE

SIMILAR FUNCTION

ThiL gene (S. typhimurium) encoding thiamin phosphate kinase can be displaced (functionally equivalent) by THI80 (S. cerevisiae), encoding thiamin pyrophosphokinase.

Comparison of the known structure of THI80 with the structure of ThiL reveals different folds. Thus, two different folds might catalyze the same reaction.

Systematic discovery of analogous enzymes in Thiamin biosynthesis. Morett, Korbel, Rajan, Saab-Rincon, Olvera, Olvera, Schmidt, Snel, Bork. Nature Biotechnology 21, 790 - 795 (2003).

MACGEFSLIARYFDRVRSSRLDVETGIG-DDCALLNIPEKQTLAISTDTL--MSEECIENPERIKIGTDLINIRNKMNLKELIHPNEDENSTLLILNQKI.* .: :: :. :::.. :. .: * *:.** * .:.:

VAGNHFLPDIDPADLAYKALAVNLSDLAAMGADPAWLTLALTLPEVDEPWDIPRPLFYKIWKLHDLKVCADGAANRLYDYLDDDETLRIKY-LPNYIIGD. :: .* . . . * * * : **:

LEAFSDSLFALLNYYDMQLIGGDTTRG-PLSMTLGIHGYIPAGRALKRSGLDSLSEKVYKYYRKNKVTIIKQTTQYSTDFTKCVNLISLHFNSPEFRSLI*:::*:.:: . .: :* * . :: :.: . . ::

AKPGDWIYVTGTPGDSAAG--LAVLQNRLQVSEETDAHYLIQR----HLRSNKDNLQSNHGIELEKGIHTLYNTMTESLVFSKVTPISLLALGGIGGRFD:: .: * :.. .: : * .*: * * ::

PTPRILHGQALRDIASAAIDLSDGLISDLGHIVKASGCGARVDVDALPKSQTVHSITQLYTLSENASYFKLCYMTPTDLIFLIKKNGTLIEYDPQFRNTC* : : . :: :.*. :** .::* .* . * : ..

DAMMRHVDDGQALRWALSGGEDYELCFTVPELNRGALDVAIGQLGVPFTCIGNCGLLPIGEATLVKETRGLKWDVKNWPTSVVTGRVSSSNRFVGDNCCF. : *:* : * .::: ..: * :. : :*

IGQMSADIEGLNFVRDGMPVTFDWKGYDHFATPIDTKDDIILNVEIFVDKLIDFL-----------*. . * .:::. * : :


3. FUNCTION AND SEQUENCE (TFBSs)

HNF1- binding sites (human)

------------AGTTAATCATTGGCC--------- -------------GTTAATTATTGGCAAATGTCCC- -------GTATGGGTTACTTATTCTCTCTTTGTTGA ------------GGTTAAGACTCTAAT--------- -------AGTCTAGTTAATAATCTACAATT------ ---------TGAGATTAATA---------------- ---------AATGATTAAAA---------------- -------------GTCAAACATTAAC---------- ----------CCGATTAACCATTAACCCCCACCCC- -------------GTTAATCAGAAAA---------- GGATGTATGTAGAATTACATAAGAA----------- -------------CTTACTCAATAAC----------

SIMILARSEQUENCE

SIMILAR FUNCTION


4. TF-MAPS: A NEW ALPHABET


5. TF-MAPS: A NEW FORM OF ALIGNMENT

MAP 1

MAP 2

We can align the TF-MAPS in this new alphabet:•Mapping score•Gaps•Positional conservation


6. TF-MAP ALIGNMENT in PROMOTER CHARACTERIZATION

TTR gene: ENSG00000118271

Pairwise TF-map alignments between TTR and 83 COREG(TTR) in CISRED

A.G. Robertson et al. cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Research, 34:D68–D73, 2006.

TTR PROMOTER RECONSTRUCTION


7. ACCURACY IN ABSENCE OF SEQUENCE SIMILARITY

The HRCZ-set(36 genes)

SEQUENCE ALIGNMENT

VsTF-MAP

ALIGNMENT


8. RESULTS

TF-map alignments are a simple reflection of sequence conservation?

Genomic region TOP 1 Avg. Score

Coding 27 3706.72

5’UTR 4 2671.78

PROMOTER 4 2005.67

3’UTR 1 1994.22

Intronic 0 1267.89

Downstream 0 1174.28

5’Intergenic 0 1052.92

3’Intergenic 0 974.69

CLUSTALW

NO

TOP 1 Avg. Score

6 17.15

2 10.48

18 25.41

7 15.85

2 8.34

0 6.85

0 5.42

1 4.14

TF-MAP ALIGNMENT

DESIGN OF THE DESIGN OF THE DATASETDATASET


9. PAIRWISE TF-MAP ALIGNMENT TRAINING

TRAINING:To systematically estimate the parameters that are globally optimal, in terms of real TFBS detection, in a set of well-annotated promoter pairs

Predictions obtained with the database TRANSFAC: V. Matys et al. TRANSFAC® and its module TRANSCompel®: transcriptional gene regulation in eukaryotes. Nucleic Acids Research 34: D108 - D110 (2006)

Plots with the program gff2ps: J. F. Abril and R. Guigó. gff2ps: visualizing genomic annotations. Bioinformatics, 8:743–744 (2000)


10. ACCURACY TESTS

REAL pair of TFBS

H

H

M

M TF-MAP ALIGNMENT

Levels:• Nucleotide• Site

Measures:• Sensitivity [0,1]• Specificity (PPV) [0,1] • Correlation Coefficient [-1,1]

Coverage

A set of experimentally annotated promoters:• The promoter sequences (mapping)• Coordinates of the real TFBSs (alignment)• TFBSs present in both promoters (alignment)

Human/Mouse orthologous genes


11. SOURCES OF INFORMATION

• General Regulatory Repositories

• Publications:- The datasets of other programs- Individual experimental works

FORMATS / QUALITY / AVAILABILITY / STABILITY


12. ABS: ANNOTATED BINDING SITES


13. MY OWN EXPERIENCE (1)

MANUAL DATA CURATION:

* FINDING THE PROMOTER SEQUENCES IN THE GENOME:1. The original promoter entry does not exist (GenBank)2. The gene has another name3. The gene has not been annotated yet (RefSeq)4. The promoter sequence does not match the current TSS (RefSeq)5. The promoter sequence is not a promoter sequence (RefSeq)

* FINDING THE MOTIFS IN THE PROMOTER SEQUENCES:1. The binding motif is not in the original promoter sequence2. The motif is not in the coordinates that it was expected to be3. The motif has changed slightly (a few nucleotides)4. There are several motifs that could correspond to the real one5. The relative position among the motifs of the same gene is wrong


14. MY OWN EXPERIENCE (2)

* TF-MAPS AND ANNOTATIONS:1. The mapping function is not defined for a given TF2. The TFBS is not predicted by the mapping function in one of the

orthologs

* MATCHING THE ALIGNMENTS AND THE ANNOTATIONS:1. There are several mapping definitions that recognize the same

motif

NEW CHALLENGES: NEW CHALLENGES: DESIGN OF FUTURE DESIGN OF FUTURE

DATASETSDATASETS


15. NON-COLLINEAR CONSERVATION


16. SITES IN OTHER SPECIES

COLLAGENASE-3 GENE (MMP13) promoters kindly provided by Dr. López-Otín (Universidad de Oviedo)


17. ENCODE ChIP data

TRANSFAC:V$E2F1_Q3

10,000 bps

mouse

human

CONCLUSIONCONCLUSION


RESEARCH ON GENE REGULATION: DUAL PERSONALITY?

COMPUTER SCIENTISTEXPERT 1

BIOINFORMATICIANEXPERT 2

EXPERIMENTALIST?EXPERT 3

RESEARCHER

[email protected]@imim.es

Documents

DESIGNING TRAINING REGULATORY DATASETS Enrique Blanco Xavier Messeguer Roderic Guigó