Here we present a database, WikiCell, as a portal for a unified view of the human transcriptome. At present, WikiCell consists of Expressed Sequenced Tags, and users may browse, query, upload and download sequences. Researchers can utilize transcriptome model based upon a human taxonomy graph. Sequences in each model are sorted by attributes such as physiological and pathological samples. The Genbank EST data format is conserved and gene information, including, house keeping genes, location and GO description, are provided.
How can I use the search engine?
You can input the name of organ, tissue or cell, or you can search by Genebank Accession Number. Let's input human taxonomy name: "bone marrow" for example:
* Step1 : Input "bone marrow" into search box which at left-middle page, and click "Go" button.
* Step2 : Bone Marrow page will show and related EST number display at "statistics" column. Go to EST summary page to click number interlink.
* Step3 : You can input page number into search page box to related summary page, such as 100.
* Step4 : If I want to browse "AV755755" data, then click the interlink.
* Step5 : AV755755 EST data will show. Genebank data show at the top, Sequence Feature and Block Feature at bottom.
How can I browse EST data?
Two ways. Firstly, browse EST data from images.
* Step1 : Click image on each body partial page, until there are data in the partial which will show number at statistics column, such as "Pineal Body", The path is Human-->Endocrine System-->Endocrine-->Pineal Body.
* Step2 : Then click the number interlink to go to summary page. Choose one Genebank Accession number and access.
* Step3 : It displays EST data page.
Secondly, browse EST data from tree graph.
* Step1 : Go to one of systems, such as motion system.
* Step2 : Click image of motion system tree graph.
* Step3 ：It displays structure graph of motion system. There are EST data of the nodes which is interlink, but not the others. Click "Pineal Body".
* Step4 : Then you can follow step2 of last method.
what does statistics mean in body partial page?
That means how many EST quantity in the body partial, including next level. EST data are classified to next level, if the quantity number could not be clicked. It will display summary page to click interlink blue number.
Which kind of data can I download and upload?
- download :
EST data, but be classified by body partial method. There are download interlink in navigation bar.
WikiCell provides EST data relative to spatial expression in the human body. You can access the ‘body path’ of the data, such as in which system, organ, tissue and/or cell the transcript is expressed. For example, if you need "bone marrow" data, access data path is /wikicelldb/Motion_System/bone_marrow/.
- upload :
Every human transcriptome data can be uploaded to wikicell. However, you must contact administrator who will look through your data, and give you right to upload the data after validating data security. If you want to upload human transcriptome data, please contact firstname.lastname@example.org.
Where is HS gene information?
On the main page, right side, you will see the HS information interlink.
Gene information are sorted into three: chromosome, HK and GO function. Briefly, through the analysis of public expression data (from ESTs and microarray data) from 18 human tissues they found that 40% of the currently annotated human genes were constitutively expressed in at least 16 of 18 tissues. We have adopted the most rigorous definition of an HK gene where a gene must be expressed in all 18 tissues examined. According to this definition, 3182 HK genes are compiled quantity statistics in each chromosome through this method.