Panther ID:11829: Difference between revisions

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[[Category:Reference Genome]]
== FOXE1/Forkhead/Forkhead box family ==
== FOXE1/Forkhead/Forkhead box family ==


==== Summary ====
==== Summary ====


[http://sourceforge.net/tracker/?func=detail&aid=1990970&group_id=36855&atid=1040173 SourceForge Link]
Gene Association File:


[http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO2OM/ORTHOMCL14416 PPOD/OrthoMCL link]
[[Media:PTHR11829forkhead.xlsx]]


==== Molecular Function ====
Note: having trouble uploading the file.  Contact Kara for the file.


Propagation:
There are annotations to be added to all Reference Genomes except for E. coli.


===== 1)  transcription factor activity (GO:0003700) =====
Related links:


Up-propagation to common ancestor node AN0, the root node, down-propagation to the following Ref Genome proteins:
[http://sourceforge.net/tracker/?func=detail&aid=1990970&group_id=36855&atid=1040173 SourceForge Link]


based on many experimental annotations, from yeast to human, that map up to the root node.
[http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO2OM/ORTHOMCL14416 PPOD/OrthoMCL link]
 
==== Molecular Function ====


===== 2)  transcription factor activity (GO:0003700) =====
===== 1)  transcription factor activity (GO:0003700) DONE =====


Up-propagation to common ancestor node AN114, down-propagation to the following Ref Genome proteins:
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.


RAT_1309196
===== 2)  protein homodimerization activity (GO:0042803) DONE  =====


CHICK_421769
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:


DANRE_ZDB-GENE-990708-6
RAT_1562112


CHICK_374231
because of positive experimental annotations to


DANRE_ZDBJ-GENE-061013-59
HUMAN_ENSG00000049768


DANRE_ENSDARG00000061549
MOUSE_MGI:1891436


RAT_1561201
===== 3)  sequence specific DNA binding (GO:43565) DONE  =====


CHICK_428703
Up-propagation to common ancestor node AN588, down-propagation to the many Ref Genome proteins (see GAF) because of positive experimental annotations to


HUMAN_ENSG00000204060
HUMAN_ENSG000000160973


MOUSE_MGI:2676586
MOUSE_MGI:1347465


RAT_1595858
MOUSE_MGI:1096329


DANRE_ENSDARG00000024619
DANRE_ZDB-GENE-000616-15


DANRE_ENSDARG00000055792
and more.


DANRE_ZDB-GENE-050116-1


because of positive experimental annotations to
==== Cellular Component:  ====


HUMAN_ENSG00000118689
===== 1)  nucleus (GO:0005634) DONE =====


MOUSE_MGI:1890081
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.


HUMAN_ENSG00000150907
No bacterial species are in this family, so erroneous annotation to 'nucleus' for bacteria is not a concern here.


MOUSE-MGI:1890077
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.'


RAT_620283


HUMAN_ENSG00000184481
===== 2)  activin complex (GO:0032444) DONE =====


MOUSE_MGI:1891915
Up-propagation to common ancestor node AN597 down-propagation to:


==== Cellular Component:  ====
RAT_1311275


===== 1)  nucleus (GO:0005634) =====
because of positive experimental annotations to


Up-propagation to common ancestor node AN20, down-propagation to the following Ref Genome proteins:
HUMAN_ENSG00000160973


MOUSE_MGI:1347465


RAT_1562112
==== Biological Process:  ====


HUMAN_ENSG000000128573
===== 1)  negative regulation of cell proliferation (GO:0008285) DONE =====


RAT_1559697
Up-propagation to common ancestor node AN175, down-propagation to the following Ref Genome proteins:


CHICK_769935
RAT_1561201


DANRE_ZDB-GENE-041203-2
because of positive experimental annotations to


HUMAN_ENSG00000137166
HUMAN_ENSG00000184481


RAT_1311386
MOUSE_MGI:1891915


DANRE_ZDB-GENE-040426-1338
===== 2)  negative regulation of cell proliferation (GO:0008285) DONE  =====


RAT_1308669
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:


CHICK_416092
RAT_1562112


because of positive experimental annotations to
because of positive experimental annotations to
Line 98: Line 100:
MOUSE_MGI:1891436
MOUSE_MGI:1891436


MOUSE_MGI:1914004
===== 3) Immune response-related annotations: DONE =====


HUMAN_ENSG00000114861 (annotated to nucleolus)
    * 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)  


===== 2)  nucleus (GO:0005634) =====
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:


Up-propagation to common ancestor node AN114, down-propagation to the following Ref Genome proteins:
RAT_1562112


CHICK_421769
because of positive experimental annotations to


DANRE_ZDB-GENE-990708-6
HUMAN_ENSG00000049768


CHICK_374231
MOUSE_MGI:1891436


DANRE_ZDBJ-GENE-061013-59
===== 4)  negative regulation of cell proliferation (GO:0008285) DONE  =====


DANRE_ENSDARG00000061549
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF)


MOUSE_MGI:1891915
because of positive experimental annotations to


CHICK_428703
HUMAN_ENSG00000184481


HUMAN_ENSG00000204060
MOUSE_MGI:1891915
 
RAT_1595858


DANRE_ENSDARG00000024619
DROME_FBgn0038197


DANRE_ENSDARG00000055792
===== 5)  insulin receptor signaling pathway (GO:0008286) DONE  =====


DANRE_ZDB-GENE-050116-1
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF)


because of positive experimental annotations to
because of positive experimental annotations to


HUMAN_ENSG00000118689
HUMAN_ENSG00000184481
 
MOUSE_MGI:1890081
 
RAT_1309196
 
HUMAN_ENSG000000150907


MOUSE_MGI:1890077
MOUSE_MGI:1890077


RAT_620283
DROME_FBgn0038197
 
HUMAN_ENSG00000184481
 
RAT_1561201


MOUSE_MGI:2676586
===== 6) determination of left/right symmetry (GO:0007368) DONE  =====


==== Biological Process:  ====
Up-propagation to common ancestor node AN588, down-propagation to


===== 1)  Immune response-related annotations: =====
HUMAN_ENSG00000160973
 
* 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 AN175, down-propagation to the following Ref Genome proteins:


RAT_1561201
RAT_1311275


because of positive experimental annotations to
because of positive experimental annotations to


HUMAN_ENSG00000184481
MOUSE_MGI:1347465


MOUSE_MGI:1891915
DANRE_ZDB-GENE-000616-15


===== 2) negative regulation of cell proliferation (GO:0008285)   =====
==== 7) ovarian follicle development (GO:0001541) DONE  =====


Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:
Up-propagation to common ancestor node AN1048, down-propagation to


RAT_1562112
RAT_1310041


because of positive experimental annotations to
because of positive experimental annotations to


HUMAN_ENSG00000049768
MOUSE_MGI:1349428


MOUSE_MGI:1891436
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:

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:

SourceForge Link

PPOD/OrthoMCL link

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

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

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