Panther ID:11829: Difference between revisions
Karadolinski (talk | contribs) |
No edit summary |
||
(25 intermediate revisions by one other user not shown) | |||
Line 1: | Line 1: | ||
[[Category:Reference Genome]] | |||
== FOXE1/Forkhead/Forkhead box family == | == FOXE1/Forkhead/Forkhead box family == | ||
==== Summary ==== | ==== Summary ==== | ||
Gene Association File: | |||
[[Media:PTHR11829forkhead.xlsx]] | |||
Note: having trouble uploading the file. Contact Kara for the file. | |||
There are annotations to be added to all Reference Genomes except for E. coli. | |||
Related links: | |||
[http://sourceforge.net/tracker/?func=detail&aid=1990970&group_id=36855&atid=1040173 SourceForge Link] | [http://sourceforge.net/tracker/?func=detail&aid=1990970&group_id=36855&atid=1040173 SourceForge Link] | ||
Line 9: | Line 20: | ||
==== Molecular Function ==== | ==== Molecular Function ==== | ||
===== 1) transcription factor activity (GO:0003700) DONE ===== | |||
Up-propagation to common ancestor node AN0 (the root node) down-propagation to many Ref Genome proteins (too many to list, see GAF file) based on many experimental annotations, from yeast to human, that map up to the root node. | |||
Up-propagation to common ancestor node | ===== 2) protein homodimerization activity (GO:0042803) DONE ===== | ||
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins: | |||
RAT_1562112 | RAT_1562112 | ||
because of positive experimental annotations to | because of positive experimental annotations to | ||
Line 27: | Line 36: | ||
MOUSE_MGI:1891436 | MOUSE_MGI:1891436 | ||
MOUSE_MGI: | ===== 3) sequence specific DNA binding (GO:43565) DONE ===== | ||
Up-propagation to common ancestor node AN588, down-propagation to the many Ref Genome proteins (see GAF) because of positive experimental annotations to | |||
HUMAN_ENSG000000160973 | |||
MOUSE_MGI:1347465 | |||
MOUSE_MGI:1096329 | |||
DANRE_ZDB-GENE-000616-15 | |||
and more. | |||
==== Cellular Component: ==== | ==== Cellular Component: ==== | ||
===== 1) nucleus (GO:0005634) ===== | ===== 1) nucleus (GO:0005634) DONE ===== | ||
Up-propagation to common ancestor node AN0 (the root node) down-propagation to many Ref Genome proteins (too many to list, see GAF file) based on many experimental annotations, from yeast to human, that map up to the root node. | |||
No bacterial species are in this family, so erroneous annotation to 'nucleus' for bacteria is not a concern here. | |||
In addition, normally I would be more conservative about propagating a component term like this, especially since there are a scattering of 'cytoplasm' annotations within the tree, but in light of the biology of this family (forkhead transcription factors), I feel comfortable in the propagation of 'nucleus.' | |||
===== 2) activin complex (GO:0032444) DONE ===== | |||
Up-propagation to common ancestor node AN597 down-propagation to: | |||
RAT_1311275 | |||
because of positive experimental annotations to | |||
HUMAN_ENSG00000160973 | |||
MOUSE_MGI:1347465 | |||
==== Biological Process: ==== | |||
===== 1) negative regulation of cell proliferation (GO:0008285) DONE ===== | |||
Up-propagation to common ancestor node AN175, down-propagation to the following Ref Genome proteins: | |||
RAT_1561201 | |||
because of positive experimental annotations to | |||
HUMAN_ENSG00000184481 | |||
MOUSE_MGI:1891915 | |||
===== 2) negative regulation of cell proliferation (GO:0008285) DONE ===== | |||
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins: | Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins: | ||
Line 43: | Line 100: | ||
MOUSE_MGI:1891436 | MOUSE_MGI:1891436 | ||
===== 3) Immune response-related annotations: DONE ===== | |||
==== | * negative regulation of interferon-gamma production (GO:0032689) | ||
* negative regulation of interleukin-10 production (GO:0032693) | |||
* negative regulation of interleukin-2 production (GO:0032703) | |||
* negative regulation of interleukin-4 production (GO:0032713) | |||
* T cell activation (GO:0042110) | |||
* negative regulation of interleukin-2 biosynthetic process (GO:0045085) | |||
* T cell activation (GO:0042110) | |||
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins: | |||
RAT_1562112 | |||
because of positive experimental annotations to | |||
HUMAN_ENSG00000049768 | |||
MOUSE_MGI:1891436 | |||
===== 4) negative regulation of cell proliferation (GO:0008285) DONE ===== | |||
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF) | |||
because of positive experimental annotations to | |||
HUMAN_ENSG00000184481 | |||
MOUSE_MGI:1891915 | |||
DROME_FBgn0038197 | |||
===== 5) insulin receptor signaling pathway (GO:0008286) DONE ===== | |||
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF) | |||
because of positive experimental annotations to | |||
HUMAN_ENSG00000184481 | |||
MOUSE_MGI:1890077 | |||
DROME_FBgn0038197 | |||
===== 6) determination of left/right symmetry (GO:0007368) DONE ===== | |||
Up-propagation to common ancestor node AN588, down-propagation to | |||
HUMAN_ENSG00000160973 | |||
RAT_1311275 | |||
because of positive experimental annotations to | |||
MOUSE_MGI:1347465 | |||
DANRE_ZDB-GENE-000616-15 | |||
==== 7) ovarian follicle development (GO:0001541) DONE ===== | |||
Up-propagation to common ancestor node AN1048, down-propagation to | |||
RAT_1310041 | |||
because of positive experimental annotations to | |||
MOUSE_MGI:1349428 | |||
HUMAN_ENSG00000183770 | |||
---- | ---- | ||
Back to [[GAFs_for_trees-based_annotations]] | Back to [[GAFs_for_trees-based_annotations]] |
Latest revision as of 15:51, 10 July 2014
FOXE1/Forkhead/Forkhead box family
Summary
Gene Association File:
Note: having trouble uploading the file. Contact Kara for the file.
There are annotations to be added to all Reference Genomes except for E. coli.
Related links:
Molecular Function
1) transcription factor activity (GO:0003700) DONE
Up-propagation to common ancestor node AN0 (the root node) down-propagation to many Ref Genome proteins (too many to list, see GAF file) based on many experimental annotations, from yeast to human, that map up to the root node.
2) protein homodimerization activity (GO:0042803) DONE
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:
RAT_1562112
because of positive experimental annotations to
HUMAN_ENSG00000049768
MOUSE_MGI:1891436
3) sequence specific DNA binding (GO:43565) DONE
Up-propagation to common ancestor node AN588, down-propagation to the many Ref Genome proteins (see GAF) because of positive experimental annotations to
HUMAN_ENSG000000160973
MOUSE_MGI:1347465
MOUSE_MGI:1096329
DANRE_ZDB-GENE-000616-15
and more.
Cellular Component:
1) nucleus (GO:0005634) DONE
Up-propagation to common ancestor node AN0 (the root node) down-propagation to many Ref Genome proteins (too many to list, see GAF file) based on many experimental annotations, from yeast to human, that map up to the root node.
No bacterial species are in this family, so erroneous annotation to 'nucleus' for bacteria is not a concern here.
In addition, normally I would be more conservative about propagating a component term like this, especially since there are a scattering of 'cytoplasm' annotations within the tree, but in light of the biology of this family (forkhead transcription factors), I feel comfortable in the propagation of 'nucleus.'
2) activin complex (GO:0032444) DONE
Up-propagation to common ancestor node AN597 down-propagation to:
RAT_1311275
because of positive experimental annotations to
HUMAN_ENSG00000160973
MOUSE_MGI:1347465
Biological Process:
1) negative regulation of cell proliferation (GO:0008285) DONE
Up-propagation to common ancestor node AN175, down-propagation to the following Ref Genome proteins:
RAT_1561201
because of positive experimental annotations to
HUMAN_ENSG00000184481
MOUSE_MGI:1891915
2) negative regulation of cell proliferation (GO:0008285) DONE
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:
RAT_1562112
because of positive experimental annotations to
HUMAN_ENSG00000049768
MOUSE_MGI:1891436
* negative regulation of interferon-gamma production (GO:0032689) * negative regulation of interleukin-10 production (GO:0032693) * negative regulation of interleukin-2 production (GO:0032703) * negative regulation of interleukin-4 production (GO:0032713) * T cell activation (GO:0042110) * negative regulation of interleukin-2 biosynthetic process (GO:0045085) * T cell activation (GO:0042110)
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:
RAT_1562112
because of positive experimental annotations to
HUMAN_ENSG00000049768
MOUSE_MGI:1891436
4) negative regulation of cell proliferation (GO:0008285) DONE
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF)
because of positive experimental annotations to
HUMAN_ENSG00000184481
MOUSE_MGI:1891915
DROME_FBgn0038197
5) insulin receptor signaling pathway (GO:0008286) DONE
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF)
because of positive experimental annotations to
HUMAN_ENSG00000184481
MOUSE_MGI:1890077
DROME_FBgn0038197
6) determination of left/right symmetry (GO:0007368) DONE
Up-propagation to common ancestor node AN588, down-propagation to
HUMAN_ENSG00000160973
RAT_1311275
because of positive experimental annotations to
MOUSE_MGI:1347465
DANRE_ZDB-GENE-000616-15
7) ovarian follicle development (GO:0001541) DONE =
Up-propagation to common ancestor node AN1048, down-propagation to
RAT_1310041
because of positive experimental annotations to
MOUSE_MGI:1349428
HUMAN_ENSG00000183770
Back to GAFs_for_trees-based_annotations