Database For Genes Implicated In Lymphoid And Myeloid Development

Question

[Dataminer]

Hi!

I am looking for a database which houses genes responsible for lymphoid or myeloid development.

Thank you,

Answer 1

[Chris Mungall]

I'm not aware of a dedicated database, but you can query GO for genes involved in lymphoid progenitor cell differentiation and myeloid cell differentiation.

(this is slightly more general than your question, as in GO 'cell differentiation' is part of 'cell development')

You also can get a gene association table for both of these terms, which includes all genes involved, together with evidence for involvement.

You can explore GO for related terms such as "myeloid progenitor cell differentiation", which may be of interest to you.

If you have questions the GO help team can answer them.

You can also explore some of the various gene signature databases. Typically these don't use controlled vocabularies or ontologies so it may be harder finding the gene sets you need, and these typically includes genes that are up or down regulated under some condition (rather than genes that have been experimentally confirmed to be involved in a core biological process). I am not an expert on these databases, but some random examples include this set from MolSigDB or these cancer gene sets from GeneSigDb.

Answer 2

[Casey Bergman]

We've developed a text-mining approach, called GETM (Gene Expression Text Miner) to associate genes with anatomical locations based on tagging of gene names and species-specific anatomy ontologies that might help with your problem.

Using this system you could search for myeloid genes using "leukocyte" as the anatomical location: http://linnaeus.smith.man.ac.uk/cgi-bin/getm/stage3.py?q_loc=leukocyte%20&loc=anat:173&loc_desc=leukocyte

Likewise, for lymphoid genes you could search with "lymph": http://linnaeus.smith.man.ac.uk/cgi-bin/getm/stage3.py?q_loc=lymph&loc=anat:685&loc_desc=lymph

Results are sorted by the number of statements supporting a gene/anatomy pairing. Excerpts of sentences from abstracts/full-text can be viewed by clicking the number in the "frequency" link.

Answer 3

[julieN]

These are not specific to to lymphoid/myeloid development but might get you on your way:

PhenExplorer: http://www.human-phenotype-ontology.org/PhenExplorer/PhenExplorer.html tab to "by ontology", choose Phenotypic abnormality > Abnormality of the hematopoietic system > Abnormality of leukocytes, etc. then right click to get genes

Jackson labs: http://www.informatics.jax.org/searches/allele_form.shtml same idea

Europhenome: http://www.europhenome.org/databrowser/viewer.jsp?advancedSearch=on&phenotype=on same idea

Molecular Hematology: http://www.blood.interhealth.info/ might be useful