Julius B. Lucks/Meetings and Notes/SMBE2007/methods comp genomics

Jeff Chuang (Boston College): Sequences conserved by selection across mouse and human malaria species

Tue Jun 26 07:54:00 EDT 2007

Talk

• 41% world pop exposed to malaria carrying mosq.
  • 1E6 deaths
• transmitted through Anopheles
  • lives in red blood cells

Plasmodium Gene Regulation

• falciparum causes most fatalities
• < 10 reg sequences characterized
• simple gene expression program
  • 80% ORFs expressed periodically in red blood cell stage
  • yeast 10% expressed in comparable stage
• small number of apparent transcription factors

Detecting Functional Sequences

• look for sequence conservation
• Genome Research, 15, 205, 2005
  • works for yeast
• Challenge 1 - phylogenetic distances between P. falciparum and other specios non-ideal
  • mouse best sequenced (3X-8X): P. berghei, P. yoelli, P. chaboudi - total dS aprox 0.5
  • comp to P. falcifarum dS >> 1
• Challenge 2 - most malaria spec extremely AT-rich genomes (> 80% AT)
  • AT cons could be due to chance
  • questionability of alignments
• PhastCons (Seipel and Haussler 2005) - phylogenitic HMM - differential mutation matrix
  • in UCSC genome browser
  • not good for malaria - saturates subst rates
• Gumby (Prabhakar, 2006)
  • conservation based scoring function using Karlin-Altschul statistics
• Regulatory Potential (Elnitski, Hardison, 2003)

Empiracal Method that Corrects for Base Composition

• intergenic sequences and orthologs
• align these (MUSCLE)
• aplly composition and conservation-dependant sccoring function to sliding windows - corrects for base comp

How much intergenic sequence conserved

• Mouse-Human 5%
• Sensu stricto yeast - 50%
• 3 mouse malariai - 2.4%
  • including falciparum - 0.1%

Harold Drabkin : Function annotation using ontologies - the Mouse Genome Informatics system uses the Gene Ontology

Tue Jun 26 07:54:38 EDT 2007

• Mouse Genome Informatics - Jackson Lab - Maine

Links

• MGI
• GO

Talk

brief summary of MGI

• genome database ...
• sequence to phenotype/disease
• manually curated experimental literature (w/ controlled vocabs)

how MGI collecs and summarizes orthology data

• homologene, inparanoid, HGNC, Tree fam
  • AA alignment, NA aling, synteny, conserved map location
• 19 species with homol to mouse genes (Human, chimp, dog, rat ...)

GO and MGI

• GO - 3 ontologies in 1
  • molecular function
  • process function participates in
  • where in cell takes place (cellular component)
• 18,000 genes, 170,000 annotations - from 8,000 papers
• directed acyclic graph - any one term can have multiple heritage
• 2 relationships
  • is a
  • part of
• GO annotation
  • statement that gene product has a part molec function, involved in a process, located in certain cell comp
  • as det by part method, described in part ref
  • GO_term:evd_code:ref
• evidence codes
  • experimental
    • ida-inferred direct assay
    • ipi-inferred phys interact.
    • imp - mutant phenotype
    • igl - genetic int.
  • predictive
    • iss - sequence or structural similarity

Reference Genome Initiative

• 12 model organisms - related to human diseases
• Graph of Ontology connections between model organisms

Questions

• defining orthologs - 1to1?
  • 1_to_1, 1_to_many, many_to_1 - up to curator

Daniel Blankenberg : Making the analyses of multiple-species whole-genome alignments accessible to everyone

Tue Jun 26 07:55:59 EDT 2007

• Nekrutenko - Penn State

Talk

Multiple Spec Alignments

• genomic align collection of local align where each sub-genomic region that aligns is a block

MAF format

• format for alignments

Alignment Manipulation

• extract alignment blocks which fall in a region
• remove species
• remove blocks
• determine coverage statistics
• convert to FASTA or other - nothing supports MAF
  • block based - multiple block - concatenated
  • interval based - start-stop - gene
• extract coding seq alignments

Galaxy

• web-based
• connection to UCSU and biomart
• 130 tools - interval operations, alignment manips, viewers, EMBOSS, hi-fi

Example

• goal: determine non-canonical mammalian genes on chrom 22
• workflow
  • obtain genomic coords for genes
  • extract mult species
  • stitch together alignments for coding exons
  • det freq of each tree

Yi Zhou : BLASTO - A tool for searching orthologous groups

Tue Jun 26 07:56:35 EDT 2007

• Landweber - Princeton
• Dept. Ecol & Evol. Biol.
• NAR, 2007
• BLASTO

Talk

• ortholog - basis for phylo inference, genome evol studies, functional annotation
• best estimated when complete genomes avail - reciprocal best hits, sim clusters
• NCBI COG - unicell org, 53 prok, 3 euk
• NCBI KOG - 7 euk
• OrthoMCL
• MultiParanoid
• TIGR EGO (DNA)
• Func annotation
  • comp gene tree - require position of quere species on ref tree
  • OrthoSTrapper
  • Rio
  • SIFTER
  • KOGnitor
• BLASTO
  • all curr well-known multi-species databases
  • no compl genome req or phylo placement of curr species
  • modified blast that treats orthol groups as a unit
  • function prediction, putative phylo relationship inference
• method
  • sig score of indiv sequences using BLAST
  • retriev orthog group information
  • comp sig score for ecah group based on indiv seq seq score
  • outputs sig score for orthog group - average likelihood of score within each group
• reduce noise comp to one-way best hits

Ian Schenk : Genomic algebra fro the masses - providing flexible operations on genomic interval data with a user-friendly web resource

Tue Jun 26 07:56:57 EDT 2007

• Nekrutenko Lab Penn State
• GalaxyOps

Talk

• genomic data
  • sequences
  • alignments
  • datapoints (scores)
  • intervals
    • chromosome, start and end - 1 dim DNA map

Gordon Plague : Nice neigbors and safe landings - orientation bias of genes flanking transposable elements in bacteria

Tue Jun 26 07:57:33 EDT 2007

Talk

• insertion sequences (ISs)
  • < 2500 bp
  • most frequent TEs in bacteria
  • QR-1RL-transposase-IRR-QR
  • prsA
• intragenic IS elements rara - knock out genes
• most IS elements intergenic
• are all intergenic regions equiv for IS insertion?
• bacterial genes have 4 diff neighboring gene orientations
  • both leading leading
  • leading-lagging
  • lagging-leading
  • lagging-lagging
• Bact genomic arch
  • most circular chromosomos
  • high coding densiting (no introns/exons)
  • org into operons
    • leu: leuL-leuA-leuB-leuC-leuD
• IS el hops into middle of gene orientations - could disrupt 1 reg region (lead-lead, lag-lag could be on same operon)
  • lagging-leading - IS could disrupt 2 promoters (setup needs to promoters)
    • hypoth - least common place for IS el to hop
  • leading-lagging - IS el cannot disrupt promoter sequences
    • hypoth - insert here the most since disrupt the most
• Y. pestis
  • 1300 - 36% - lead lead
  • 546 - 15% - lead-lag
  • 579 - 16% - lag-lead
  • 1183 - 33% - lag-lag
• data supports both hypotheses