Gene families gene/protein families

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Annotation notes

  • JGI BLAST searches are run with a 10-7 cutoff
  • see JGI naming conventions for more information on what the JGI model names mean. The numerical model ID is the most reliable way to identify specific gene models as the name can be changed.

JGI browser hints

  • in the scaffold track, Red = gaps in assembly, black = contigs
  • in the Vista tracks, pink= intron/intergene space, blue=exon
  • "needs GO" on the transcript annotation page means that there is no appropriate GO term. Do not use this to indicate that GO terms have not been assigned.

Naming Genes

  • Do not include prefixes such as selmo or smo
  • use a suffix -1 or -2 to indicate the two alleles,for example, CPK5-1 and CPK5-2
  • use a three or four letter code followed by a number (such a a gene symbol) for the gene name
  • if practical or sensible, try to follow numbering of other plants,

Assignments

Please list the genes, protein families, or other aspects of the genomic sequence that you are committed to working on. Follow the kinase example - it's easy! Note that you have to be logged in to edit pages, see the upper right corner of any page.

Example

Feel free to add to or change this table. The wiki system allows us to recover the old version if you make a mistake. For those new to wikis, here is a hint on editing the table.

A simple version of the table looks like this

{| border="1" cellspacing="0" cellpadding="5"
|- style="1px solid black;"
| Investigator
| Email
| Annotation focus
|-
| Jody Banks
| banksj@purdue.edu
| flagella
|}

the table begins and ends with {| and |}. You can ignore anything that follows the {|; these are formatting commands. In between, the information for each line of the table begins with |-, and each column follows with the information for each column appearing on a separate line beginning with |. So, to add my entry I would add the following before the closing |} line

|-
| Michael Gribskov
| gribskov@purdue.edu
| protein kinases

Assignment Table

If you don't see the edit tab at the top of this page, you must log in first to edit. The tab will then appear.

The order of names and topics in this table have absolutely no significance - please do not get bent out of shape if you are not where you would like to be (feel free to change the table). This table was mostly created by Jody from people's emails, and then converted to the wiki, but in the process was merged with a separate list I had started. If you indicated an interest in more than one family, you probably have entries in multiple sections of the table - we have tried to not arbitrarily remove anyone's innterests. A yes in the fourth column means that you have already worked on this gene family in selaginella. Due to merging Jody's material and mine, there are also some comments about possible collaborations in this column.Gribskov 15:39, 20 September 2007 (EDT)

I'm thinking that we may want to appoint leaders or a establish working groups for broad categories such as protein kinases or transcription factors to handle the details of who is doing what and to make sure that things advance expeditiously. Suggestions on how to do this are welcome.Gribskov 15:39, 20 September 2007 (EDT)

Hormones (see also signaling)
Aldwin Anterola anterola@plant.siu.edu terpene synthases
isoprenoid pathway genes
gibberellin biosynthetic genes
possibly Dr. Sinha on gibberellin biosynthetic genes
Cédric Finet Cedric.Finet@ens-lyon.fr Auxin Response Factors (ARFs), auxin signaling enzymes (YUCCA, CYP79B2, AAO1...)
Guichuan Hou houg@appstate.edu genes that function in root development, such as homologs/analogs (if any) in the GRAS and PIN families Mike Barker?
Neelima Sinha nrsinha@ucdavis.edu GA biosynthesis genes
Rathinasabapathi,Balasubramani brath@ufl.edu glutaredoxins and genes in the biosynthesis of pantothenate and beta-alanine
Alexander Heyl
Birgit Pils
heyl@zedat.fu-berlin.de
pils@well.ox.ac.uk
cytokinin signaling components
Victor Albert victor.albert@nhm.uio.no ABA receptors
Tomomichi Fujita tfujita@sci.hokudai.ac.jp ABA, Brassinosteroids, ethylene yes
Naoki Shinohara shino@nibb.ac.jp auxin yes
Minoru Kubo ku-bo@nibb.ac.jp cytokinin yes
Tomoaki Nishiyama tomoakin@kenroku.kanazawa-u.ac.jp all
Protein kinases and signal transduction related genes
John Williams Mundy MUNDY@adm.ku.dk MAPKs, MAP2Ks, MAP3Ks
Jake Stout stout0@purdue.edu G-protein alpha, G-protein beta, G-protein coupled receptors
Gerard Manning
Michael Gribskov
manning@salk.edu
gribskov@purdue.edu
all yes
Martin Potocky potocky@ueb.cas.cz phospholipid and phosphoinositide signalling genes
Neelima Sinha nrsinha@ucdavis.edu Aux/IAA family
Eric Engstrom emengs@wm.edu GRAS genes, ethylene signaling genes
Chi-Kuang Wen cwen@sippeac.cn ethylene signaling genes,
Hong Ma hxm16@psu.edu Cyclins and CDKs
John Larkin jlarkin@lsu.edu CDK inhibitors, both SIM-like and KRP-like, and Cyclins, CDKs, and other cell cycle genes
Masaki Ishikawa ishikam@nibb.ac.jp Cell cycle yes
Michael J. Prigge mprigge@indiana.edu Auxin signaling (TIR1/AFB, ARF, Aux/IAA, PIN, AUX1/LAX, PINOID-like, YUCCA/FLOOZY, Trp aminotransferase, GH3, IRL1/ILL, SAURs(?), IAN Nitrilase-like, ABP, AXR4, IBR5, DIAGEOTROPICA, Class III HD-Zips, TOPLESS, SGT1, AXR1-like (and other SCF-concerning components), Inositol kinases)
Aldwin Anterola anterola@plant.siu.edu Lipoxygenase/Jasmonate pathway genes
Sheila McCormick sheilamc@nature.berkeley.edu Rop-GEFs, other signaling components in RLK pathways
Saori Miyazaki saori@nibb.ac.jp development related Receptor like kinases
Tomoaki Nishiyama tomoakin@kenroku.kanazawa-u.ac.jp all related to development
Transcription factors
Bernd Mueller-Roeber bmr@rz.uni-potsdam.de all Diego Riaño (diriano@uni-potsdam.de), Luiz Gustavo Guedes Corrêa (correa@uni-potsdam.de)
Stefan Rensing stefan.rensing@biologie.uni-freiburg.de all
Neelima Sinha nrsinha@ucdavis.edu KNOX genes
Zengyan Xie xiezy@mail.cbi.pku.edu.cn HAP3 genes
Jill Harrison jill.harrison@plants.ox.ac.uk genes involved in meristem function yes
Tsuyoshi Aoyama t_aoyama@nibb.ac.jp Shoot meristem, axillary meristem, Root and lateral root yes
Guenter Theissen guenter.theissen@uni-jena.de MADS-box genes
Victor Albert victor.albert@nhm.uio.no TCPs, and YABBY-like genes yes
Patricia Springer pspringer@ucr.edu LBDs, and perhaps help with MYBs, bHLHs, GRAS domain, and others
Hong Ma hxm16@psu.edu bHLH, possibly Myb, possibly homeodomain, Cohesins and condensins, Proteosome and ubiquitination pathways, SKP1, F-box genes, ubiquitin, SUMOs, etc.
Elizabeth Barker barker.e@gmail.com MADS-box and KNOX yes
Amy Litt alitt@nybg.org MADS-box, AP2/ERF
Erik Vollbrecht vollbrec@iastate.edu C2H2 zinc finger proteins
Barbara Ambrose b.ambrose@massey.ac.nz MADS-box
Christian Schulz Christian.Schulz-3@ruhr-uni-bochum.de; cschulz@nybg.org MADS-box
John Mundy MUNDY@adm.ku.dk, mcs@bio.ku.dk, simonb@bio.ku.dk WRKY protein family
Minoru Kubo ku-bo@nibb.ac.jp vascular development
Tomoaki Nishiyama tomoakin@kenroku.kanazawa-u.ac.jp all related to development
Transporters and membrane proteins (except receptor protein kinases
Michael Gutensohn gutensohn@pflanzenphys.uni-halle.de chloroplast protein transport machineries; components of the Toc and Tic machineries involved in the the translocation of nuclear encoded chloroplast proteins across the two chloroplast envelope membranes
Alonso Rodriguez-Navarro alonso.rodriguez@upm.es potassium and sodium transporters
starting with HKT and HAK continuing to potassium channels and K-Na/H exchangers
Ingo Dreyer dreyer@uni-potsdam.de K channels and cyclic nucleotide gated channels (CNGC) yes
Uener Kolukisaoglu uener.kolukisaoglu@uni-rostock.de ABC transporters
Burkard Schulz bschulz@purdue.edu ABC transporters yes
Jeff Gustin jgustin@purdue.edu Cation Diffusion Facilitator (CDF) Family
Sylvie Lalonde & Wolf Frommer wfrommer@stanford.edu glucose and sucrose transporters
Dominique Loque & Wolf Frommer wfrommer@stanford.edu ammonium transporters
Koji Mikami Phosphoinositides (PIs) komikami@fish.hokudai.ac.jp yes
Nakako Shibagaki NShibagaki@lbl.gov sulfate transporters
Chromatin proteins/RNAi associated proteins
Carolyn Napoli cnapoli@Ag.arizona.edu all
Lingjing Chen lchen2@nature.berkeley.edu polycomb group(PcG) genes
Mari Obara mobara@nibb.ac.jp RISC complex, epigenetics yes
Yasuko Oguri yoguri@nibb.ac.jp epigenetics yes
Sachiko Wakazuki mo_wakazuki@yahoo.co.jp epigenetics yes
Tomoaki Nishiyama tomoakin@kenroku.kanazawa-u.ac.jp all
MicroRNA and small RNA-producing regions of the genome
Michael Axtell mja18@psu.edu all, including microRNA target predictions yes
DNA recombination and repair
Cliff Weil cweil@purdue.edu all
Dorothy Shippen dshippen@neo.tamu.edu all, plus telomere related genes
Hong Ma hxm16@psu.edu RAD50, RAD51, RAD52, RAD54, RAD55, RAD57, etc, and MSHs, MLHs, DNA helicases, ligases
Light
Ken Karol kkarol@nybg.org cryptochromes, phytochromes and phototropins
Todd P. Michael tmichael@waksman.rutgers.edu circadian, light signaling and flowering time genes
Dion Durnford durnford@unb.ca Light-harvesting complexes and relatives (ELIPs, SEPs, OHPs). Light-stress related genes.
Yoshikatsu Sato yoshi@nibb.ac.jp Light signaling and Circadian clock yes
Tadayoshi Hirai thirai@gene.tsukuba.ac.jp Light signaling and Circadian clock yes
Nagisa Sugimoto nagisa91@nibb.ac.jp Light signaling and Circadian clock yes
Secondary Metabolism
Clint Chapple chapple@purdue.edu cytochrome P450-dependent monooxygenases, serine carboxypeptidase-like proteins, BAHD acyltransferases, all enzymes of phenylpropanoid metabolism yes
Victor Albert victor.albert@nhm.uio.no chalcone/pyrone synthase and related downstream pathways (but...considerable overlap w/ Clint Chapple)
Seiichi Matsuda matsuda@rice.edu sterol and triterpene Biosynthesis
Minoru Kubo ku-bo@nibb.ac.jp vascular development (Lignin etc.)
Transposable elements
Jeff Bennetzen maize@uga.edu all
Primary metabolism
Victor Albert victor.albert@nhm.uio.no cytochrome c oxidase subunits, other proteins in the respiratory pathway
Jin Miao jin.miao@pku.edu.cn Glutaredoxin family genes
Uener Kolukisaoglu uener.kolukisaoglu@uni-rostock.de C2 cycle genes and amino acid racemases
Bala Rathinasabapathi brath@ufl.edu glutaredoxins, pantothenate and beta-alanine biosynthesis
Mitochondrial genome
Ken Karol kkarol@nybg.org all
Victor Albert victor.albert@nhm.uio.no coding
Chloroplast genome
Ken Karol kkarol@nybg.org genes that are typically found in the plastid genome but have been lost in the Selaginella cp genome yes
Cell biology
Alison Roberts aro1844u@postoffice.uri.edu Cellulose synthase superfamily yes
Henrik Scheller hscheller@lbl.gov cell wall related glycosyltransferases (excl GT2)
John Fowler fowlerj@science.oregonstate.edu ROP GTPase-related genes (eg, ROPs, RICs, etc),select genes related to vesicle trafficking (exocyst, possibly some Rabs) and in the actin cytoskeleton
Marek Elias melias@natur.cuni.cz Ras superfamily GTPases (including ROPs and RABs)
Burkard Schulz bschulz@purdue.edu immunophilin genes, FKBPs and cyclophilins yes
Takashi Murata cytoskeleton tkmurata@nibb.ac.jp yes
Jody Banks banksj@purdue.edu flagella proteins (and other genes lost in the angiosperm lineage)
Hong Ma hxm16@psu.edu Motor proteins, kinesins, myosins, dyneins
Robert Pruitt pruittr@purdue.edu organ fusion genes (fiddlehead, hothead, etc.)
Genome Evolution
Stefan Rensing stefan.rensing@biologie.uni-freiburg.de large scale duplication issues
Mike Barker msbarker@indiana.edu Gene and genome duplications
Stefan Rensing stefan.rensing@biologie.uni-freiburg.de Comparison to Physcomitrella & synteny
John Cushman jcushman@unr.edu Comparison to S. lepidophylla, transcriptome comparisons; LEA genes
Mel Oliver Mel.Oliver@ars.usda.gov transcriptome comparisons
Mike Barker msbarker@indiana.edu evolutionary stats for gene families (Ka, Ks, Ka/Ks,and NJ and ML trees)
Victor Albert victor.albert@nhm.uio.no intragenic repeats
Tomoaki Nishiyama tomoakin@kenroku.kanazawa-u.ac.jp Conservation and diversification of genes related to development.
Genes of unknown function
John Williams Mundy MUNDY@adm.ku.dk Genes of unknown function
Sporogenesis and gametogenesis
Harry T Horner hth@iastate.edu sporogenesis
Sheila McCormick sheilamc@nature.berkeley.edu gametophytes
Saori Miyazaki saori@nibb.ac.jp homologues of pollen development related genes
'Flowering time' genes; promoters/repressors of reproduction
Victor Albert victor.albert@nhm.uio.no all; would also like to cooperate! yes
RNA recognition motif (RRM) containing proteins
Victor Albert victor.albert@nhm.uio.no all
WW domain containing proteins
Victor Albert victor.albert@nhm.uio.no all
Pentatricopeptide repeat (PPR) motif containing proteins
Mamoru Sugita sugita@gene.nagoya-u.ac.jp all yes
Development related genes (functional aspects rather than gene family)
Yuji Hiwatashi hiwatash@nibb.ac.jp Shoot meristem and axillary meristem yes
Tsuyoshi Aoyama t_aoyama@nibb.ac.jp Shoot meristem, axillary meristem, Root and lateral root yes
Tomomichi Fujita tfujita@sci.hokudai.ac.jp Seeds
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