manual - Kahi Kai
Contents
1. Welcome Eric R ttinger Logout GENE INFORMATION Gene name and synonyms Brachyury Bra Species Ptychodera flava Gene added by Eric R ttinger on 23 Sep 2008 Papers about this gene Tagawa K 1998 and Peterson KJ 1999 Comments about this gene Be the first to comment on this gene Please choose the experiment design If you have done any kind of perturbation experiment you should first add a wild type control experiment and then add the treatment as a separate experiment that is linked to the control If you choose any other design than wild type you will be asked to link that to a control in the next step Experiment design type Wildtype Please choose the type of assay used for detection of the expression Assay type RNA in situ Save you can add gene RNA in situ or Immunohistochemistry experiments you can add gene expression patterns performed on microinjected drug treated embryos etc the only thing you have to specify first is a wild type gene expression pattern kahikai Comparative Marine Invertebrate Gene Expression Database _ adding a new experiment Il image upload REVIEW IMAGES AND ASSIGN STAGES 5 6 for the image upload please follow the l Ee guidelines described above you can upload several pictures at a time and assign the developmental stage and view in the next sian Egg step Not Available Not Available Not Available Not Available Not Avai2. kahikai Comparative Marine Invertebrate Gene Expression Database BET T manual Tha 3 Ce p FIDA dxipgps Jor marg TOE Yo GA PEE and DIRE gets tee pare based qe q 4w grece camp ORE the eee B Qo n o 47 apport ee Tog Db Gh pubem cs mPa purmmpas PEdde GERE gi BS inet pe a Be dopy er I vox TALA bi REG ncs Tee B3 Ph oor Lec D I Meu Cees Beer C4 bee SEARCH Search Ey gena name Tange geo mam IIT ED A3 aper Search Search by stage and expression eras Bat ee AA ijprert DATABASE INFORMATION Number of species Number of genes t Number of capone ae Number of images LEA Tool Word rea grow dg rapa BES Fr d Omatiasormeradggmalcoem kahikai Comparative Marine Invertebrate Gene Expression Database _summary querying the database 1 search by gene name 2 advanced search 3 query results 4 query result part 9 query result part Il RECENTLY ADDED SPECIES We aw adding editing information 1 overview 2 general guidelines 3 adding a gene 4 vs kahikai Comparative Marine Invertebrate Gene Expression Database _ search by gene name tools introduction gene expression species marnes stations Z SEARCH DATABASE INFORMATION gt Search by gene name Number of species database information about the enter a gene name and select one TC ES ia a Md RE number of species genes all species
3. m Add new species Select species Nematostella vectensis ri Search Select species All species Search Search by stage and expression domain Search by stage and expression domain Select species Nematostella vectensis Update Select species All species E Update Please select stages and domains to the right before you submit the search Please select stages and domains to the right before you Select developmental stages Select expression domains submit the search Select developmental stages Select expression domains Search Egg Animal Search LJ Egg LJ Animal O Cleavage O Vegetal Egg l Animal hemisphere 3 Blastula O Ectoderm Cleavage _ Animal pole O Gastrula O Endoderm J Cleavage Vegetal Blastula _ Vegetal hemisphere search ALL Blastula Vegetal pole Gastrula Ectoderm larval stages j gt Early Gastrula Apical tuft ectoderm Larval Embryo LJ Mesoderm Adult _ Germ cells Late Gastrula Base of tentacle ectoderm _ Mid Gastrula Body wall ectoderm A L L S D e C e S Larval Embryo ntratentacular ectoderm Searc h on ly 0 N E Early Planula Mesentery Ectoderm T I Late Planula Oral Ectoderm specific larval stages I Planula 3 Pharyngeal ectoderm list of simplified developmental stages and gene expression 5 E Adult Tip of tentacles ectoderm domains optimized for inter species Early juvenil Endoderm comparison Juvenile Apical tuft endoderm _ Tentacle bud Tentacle
4. of interest for a search ee tnum si experiments and images added to by gene name Se E ame 2 ania RESI USE expression patterns Search by stage and expression domain PRET EEE Y EREI use the buttons in the tool section to select one all species for a ap pne pps ov e EI eee 2 _add a new gene advanced search en _add anew species m Add new species click on the arrows to geta RECENTLY ADDED SPECIES mam 6complete list of species from which gene expression data are available list of recently added species i aW is 11 2008 SERTC SCONR click on the arrows to geta complete list of all genes from which gene expression data are available RECENTLY PUBLISHED GENES click the gene name Species Added by alle vec Patricia Lee on 15 Jan 2009 click the species name Pi 3 Eric R ttinger on 14 Jan 2009 Eric R ttinger on 13 Jan 2009 ET Tropo M yi Kevin Pang on 9 Jan 2009 amp B U add an experiment click the author name EN SNR ida _edit the gene MES delete the gene RECENTLY ADDED LABS List of labs that have recently joined and contributed to the database kahikai Comparative Marine Invertebrate Gene Expression Database _ advanced search tools introduction gene expression species marine stations SEARCH TOOLBOX SEARCH TOOLBOX Search by gene name Genes Search by gene name Genes m Add new gene m Add new gene Enter gene name Enter gene name Species m Add new species Species
5. of your lab in addition you can create a group invite people outside your lab to that group and share experiments with them if you are the person who added the gene experiment to the database you have the authorization to edit them at any time if you wish to edit gene experiment information not added by you please contact the submitting person in case there are other problems please contact us and we will try to resolve them as soon as possible kahikai Comparative Marine Invertebrate Gene Expression Database _ general guidlines In order to get a homogenous and easy to use gene expression database please use the following guidelines to add new gene expression patterns 1 for optimal performance of the database and to get most out of it please provide as much information as possible 2 please cite correctly the original work and where the uploaded experiments are coming from 3 if possible the picture you upload should be square and cropped to have as little empty space as possible and be not bigger than 3000x3000px or 4mb the picture can be in tiff or jpg 4 please orient the pictures always the same within a species if possible and depending on the stages the animal pole and the dorsal side should be up the vegetal pole and the ventral side should be down the anterior and the oral side to the left and the posterior and aboral side to the right of course these guidelines may vary depending on the view pro
6. value the lower the similarity _check the boxes of several or all genes to compare their expression pattern _click on the gene name to view the single gene expression pattern if information about gene ontology pathways and orthologs are available for your species and provided by the genome sequencing center please submit this information in order to allow us to implement this information in the database if this information and a protein Id have been provided while adding the gene to the database these data will be automatically retrieved and shown in this section field to leave a comment visible to all users kahikai Comparative Marine Invertebrate Gene Expression Database _ query result ahikai Welcome Eric Rominger Locost overview of all available information concerning the given tools gene expression image IMAGE INFORMATION GENE INFORMATION TOOLBOX S G d l asas NE cra you are able to visualize and even download a high Mid Gastrula Anthoxl NvAx1 and posterior hox m Download hi res image Edit image resolution image for your personal use View Species m Delete image i Lateral Nematostella vectensis cum please contact the person who uploaded the image to the Species Gene added by m Add new gene database and credit the person accordingly if you wish to Nematostella vectensis Kevin Pang on 20 Aug 2008 i Species use the image for presentation publication these images Image add
7. and 2 domains O Post hatching No images O Tonaria larva 1 images and 1 domains O Agassiz No images LJ Juvenile No images LJ Adult No images kahikai Comparative Marine Invertebrate Gene Expression Database _ adding a new experiment IV publishing or sharing the data at this point you can decide if you wish to publish your experiment to allow all the KahiKai members to appreciate your work or to keep it unpublished in the latter case only you the lab members and the website administrators are able to see your data in order to promote interactions and communication we added a feature allowing you to invite members not belonging to your lab to share selected expression pattern experiments to do so you have to create a group in your settings define it as a lab project and then invite all the persons you wish to join this group all non published experiments and of course published patterns associated to that lab project group will be visible to the group members TOOLBOX Brachyury m Add experiment m Edit Brachyury Experiment E Edit experiment B Add new gene Species m Add new species 1 select your experiment 2 select the lab project you wish to add the experiment to ADD TO PROJECT Project No project Add Cancel ADD TO PROJECT Proiect Dro Ptychodera flava Cnidarian D V axis Add Cancel kahikai Comparative Marine Invertebrate Gene Expres
8. atabase _ adding a new experiment general information ahikai tools ADD EXPERIMENT E ae nape existing experiment choose one Available experiments on Brachyury Experiment gt 1 Experiment information Experiment details Publications Choose images Review images and assign stages j Add expression information amp Experiment 1 by Eric R ttinger Cancel EXPERIMENT INFORMATION 1 6 You will automatically be assigned as author of the Please write a short description of your experiment experiment However if you add an experiment which was done by someone who is not a user of this website you could either invite him and let him add his own data or you could just add his name in the field below Description Remember that you will still be the contact person if someone have questions about the experiment Added by Eric R ttinger Author if other than yourself You have to specify in which lab you did this experiment To add your labs to the list below you first have to check if your lab exists in our community You can do that by searching on the community page and if it already exist you can send an application to join this is a necessary security measure since all labmembers of a lab can see unpublished data If the lab does not exist you can create a new labgroup in your settings You can t add your experiment unless a lab is specified Lab Please choose one of the following labs
9. ectoderm Base of tentacle endoderm Body wall endoderm Mesentery Endoderm Pharyngeal endoderm Tentacle endoderm check the boxes corresponding to the and or Selected species of interest click the SEARCH button to view the query results in all species or in one given species list of all developmental stages and gene expression domains optimized for the given species kahi Comparative Marine Invertebrate Gene Expression Database _query results manne statons SPECIES INFO DATABASE INFORMATION Name Number of species Nematostella vectensis Starlet sea anemone 10 Taxon Number of genes Cnidaria 81 Added by Number of experiments Mattias Ormestad on 11 Jan 2008 84 Papers about this species Number of images No papers added yet 584 Tools Add new gene Add new species RECENTLY PUBLISHED GENES FOR THIS SPECIES Gene Species Added by Tct Nematostella vectensis Patricia Lee on 15 Jan 2009 Brachyury Nematostella vectensis Mattias Ormestad on 25 Nov 2008 Wnt3 Nematostella vectensis Mattias Ormestad on 25 Nov 2008 FoxA Nematostella vectensis Mattias Ormestad on 25 Nov 2008 Bm m M 0 n Otx8 Nematostella vectensis Mattias Ormestad on 15 Oct 2008 Compare selected list of recent added genes for the given species click the arrows on the right to get a complete list _check the boxes of several or all genes to compare their expression pattern _click on the gene name to view the single gene expres
10. ed by Papers about this gene Add new species 3 Kevin Pang on 20 Aug 2008 No papers added yet are not for commercial use in any case Comments about this gene Be the first to comment on this gene IMAGE DATA Anthox1 Mid Gastrula stage Latera view Expression Vegetal pole Image description N A Experiment description N A kahikai Comparative Marine Invertebrate Gene Expression Database how to enter data to the database overview In order to be able to add data to the database website and for security reason you have to be a registered member if you wish to add a new species to the database please use the species request form follow the instruction by providing as much details as needed and we will add the new species to the database as soon as possible to add a new gene to the database please use the new gene feature in the toolbox and follow the instructions for a good performance of the database please use the general gene name no abbreviations and add synonyms If available to add a new experiment wild type drug treatment injection etc associated to a given gene please select the add experiment feature in the gene specific toolbox and follow the Instructions after adding a new experiment you can decide to publish it allowing all KahiKai members to see the experiment or maintaining it unpublished in the latter case the experiment will only be visible by the members
11. information about the gene such Gene name Genes as name synonyms and species in the window below No gene selected Add new gene 1 please enter a general gene name The second step of the process is to start adding your Species 7 s iiia Add new species and its synonyms if available and wae select the species for which you 2 Publications 1 Cancel wish to add the gene 2 if available please provide the reference s in which the gene expression Is discussed GENE INFORMATION 1 2 Gene name Synonyms separate by comma Species Nematostella vectensis Gene ID optional Protein ID optional Save kahi If you wish to add a new experiment to the database please provide as much details as possible 1 enter general information about the experiment 2 you have to specify in which lab this experiment was performed to add your labs to the list below you first have to check if your lab exists in our community You can do that by searching on the community page and if it already exist you can send an application to join this is a necessary security measure since all lab members of a lab can see unpublished data If the lab does not exist you can create a new labgroup In your Settings You cant add your experiment unless a lab is specified 3 please provide experimental details 4 upload information pubmed ID for publictions if available Comparative Marine Invertebrate Gene Expression D
12. lable 1 after the picture upload all new Images will appear above the gene expression pattern ready to be assigned to a given developmental stage Not Available sa Not Available Not Available 2 by clicking on the selected picture a popup window will appear allowing you to enter information about the stage and the view you can also delete the image 3 after saving you Information the picture will appear in the gene expression pattern at the defined position 4 to edit please click on the picture CN R E IMAGES AND ASSIGN STAGES s e All images have already been assigned to stages please continue to the next step to add expression data and the pop up window will appear mC allowing you to modify your entries m a Cores Not Available Not Available Not Available e Not Available Not Available Lc Not Available Not Available Not Available the last step to add a new experiment is to provide accurate gene expression information this information is highly important for the functioning of various features of the database eg query by expression domain automatic search for synexpression groups etc green squares Indicate stage for which expression information Is available red squares indicates the absence of information black squares Indicate no expression for that stage white squares indicate no data image for that stage 1 by clicking on the stage next to the red new entry or gree
13. les endoderm hemisphere Base of tentacle endoderm al cal Apikal tuft endoderm Base of tentacle ectoderm Body wall ec foderm Body wall endoderm Intratentac ular ec foclerm Mesenfery Ec tocderm Mesenfery Encocerm Oral Ec foderm Tentacle ectoderm Tenfacle encdoderm Tip o Pharyngeal ectoderm Pharyngeal endoderm Apical tuft ectoderm 9 2 a a E 2 ie E E lt L Animal pole Vege Vege Tip o Early Gastrula Mid Gastrula Late Gastrula Early Planula Planula Late Planula Tentacle bud Early juvenile Juvenile Expression Ambiguous expression No expression Not determined grid view of gene expression for one given gene the rows left represents the developmental stages the columns upper part the defined expression domains color code as indicated in legend mouse over the colored box shows the expression information and clicking on the colored box leads to the corresponding images overview of available pictures representing the gene expression pattern pictures with blue arrows underneath indicate a stack of pictures click on the arrows to get the next view click on the image itself to get a bigger view and more details kahi _ query result GENES WITH A SIMILAR EXPRESSION PATTERN Gene MoxA Anthox7 NvHD060 Gbx Wnt16 Anthox8b Anthox6 Rough Msx Msx2 Wnt3 Hedgehog dopa beta monooxygenase Compare with current Species Nematostella vectensis Nematostella vecte
14. n square edit a detailed list of gene expression domains will appear please select the corresponding information and save you entry 2 now the red square should be turned into green you re done _ adding a new experiment Ill expression information ADD EXPRESSION INFORMATION 6 6 Adding expression data Egg No images oO Cleavage No images O Blastula No images Early Gastrula No images O Mid Gastrula No images O Late Gastrula No images C Pre hatching 1 images and 0 domains O Post hatching No images Tonaria larva 1 images and 1 domains O Agassiz No images LJ Juvenile No images U Adult No images kahi Comparative Marine Invertebrate Gene Expression Database Expression domains There is no data added for this stage yet If there is no expression please save the form to confirm Animal f Animal hemisphere C Animal pole Vegetal f Vegetal hemisphere O Vegetal pole Ectoderm Aboral ectoderm Anus Apical tuft Blastopore Dorsal ectoderm Dg a amp G 0 ogo Dorsal nerve cord Hydropore Neotroch Oral ectoderm Postoral ciliated band Stomodeum Telotroch Ventral ectoderm ng mg mg mu mg Ventral nerve cord ADD EXPRESSION INFORMATION 6 6 Adding expression data O Egg No images O Cleavage No images O Blastula No images C Early Gastrula No images O Mid Gastrula No images O Late Gastrula No images Pre hatching 1 images
15. nsis Nematosfella vectensis Nematostella vectensis Nematostfella vectensis Nematostella vectensis Nemafostella vectensis Nematostella vectensis Nematostella vectensis Nematostella vectensis Nematostella vectensis Nematostella vectensis Nematostella vectensis Nematostella vectensis Nematostella vectensis Nematostella vectensis GENE ONTOLOGY PATHWAYS amp ORTHOLOGS part II Added by Kevin Pang on 14 Oct 2008 Kevin Pang on 20 Aug 2008 Kevin Pang on 25 Aug 2008 Kevin Pang on 14 Oct 2008 Kevin Pang on 14 Oct 2008 Kevin Pang on 20 Aug 2008 Kevin Pang on 30 Nov 1 Kevin Pang on 14 Oct 2008 Kevin Pang on 14 Oct 2008 Kevin Pang on 14 Oct 2008 Kevin Pang on 14 Oct 2008 Kevin Pang on 30 Sep 2008 Kevin Pang on 30 Sep 2008 Mattias Ormestad on 25 Nov 2008 Eric R ttinger on 22 Sep 2008 Heather Marlow on 11 Aug 2008 No protein id has been added for this gene so we are unable to check our GO dataset No protein id has been added for this gene so we are unable to check our KOG euKaryotic Orthologous Groups dataset No protein id has been added for this gene so we are unable to check our EC dataset COMMENTS No comments have been added yet Add a comment Title Comment Add comment Comparative Marine Invertebrate Gene Expression Database list of genes with a similar expression pattern automatically created based on the informations provided by the users while adding gene expression data to the database the lower the
16. sion Database we hope that you will enjoy using the database if you have any suggestions about how we can improve this gene expression database or if you have any concerns regarding this project please feel free to contact us any time m ormestad amp e roettinger mattias dkahikai com eric dkahikal com
17. sion pattern kahi Comparative Marine Invertebrate Gene Expression Database _ query result part list of experiments added for the gene in the given species tools introduction gene expression species manne stations click on the Experiment bar to view all available experiments GENE INFORMATION EXPERIMENTS OBP5OX Gene name and synonyms Available experiments on Anthox1 Anthox1 Anthox1 NvAx1 and posterior hox Experiment Add experiment ure M T a Edit Anthox toolbox to add experiments edit the given gene add a new gene and Nematostella vectensis Experiment 1 by Kevin Pang Genes request the implementation of a new species Add new gene Gene added by j Kevin Pang on 20 Aug 2008 Species Add new species Papers about this gene click to expand and No papers added yet Comments about this gene view the whole experiment set EXPRESSION SUMMARY Be the first to comment on this gene Showing only wildtype data for Anthox1 IMAGES Showing only wildtype data for 1 experiments on Anthox1 Click on experiments above to show data from only that particular experiment Egg Cleavage Blastula Early Gastrula Mid Gastrula Late Gastrula Lateral View Lateral View Lateral View Lateral View t gt Early Planula Planula Late Planula Tentacle bud Early juvenile Juvenile Lateral View Lateral View Lateral View Lateral View Lateral View Lateral View J M plate presumptive endoderm enfacles ectoderm enfac
18. vided animal right right ventral posterior ventral dorsal anterior ci dorsal vegetal left kahi Comparative Marine Invertebrate Gene Expression Database _ adding a new species If you wish to add a new species to the ahikai a database please provide as much details as possible using the add species form ADD SPECIES TOOLBOX Add species text TERR P 1 Species information Add new gene 2 Species thumbnail 3 Developmental stages Species f enter general and genomic 4 e domains Add new species information if available for the given aoe species 2 provide a high quality picture representing the new species SPECIES INFORMATION 1 5 Requested by enter user ID Latin name 3 provide a detailed list of developmental stages rm modifications need to be done by us TaxonID Taxon 4 provide a detailed list of expression domains modifications need to be done by us Base URL for links to gene ID s Link to genomic database Save 5 if available please provide a general reference about the species kahi Comparative Marine Invertebrate Gene Expression Database _ adding a new gene If you wish to add a new gene to the kahikai Welcome Eric R ttinger Logoa database please provide as much details as possible ADD GENE GENE INFORMATION 1 TOOLBOX Adding a new gene to the database is a simple two step process First you enter
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