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 AN20, down-propagation to the following Ref Genome proteins:
[http://sourceforge.net/tracker/?func=detail&aid=1990970&group_id=36855&atid=1040173 SourceForge Link]


RAT_1562112
[http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO2OM/ORTHOMCL14416 PPOD/OrthoMCL link]


HUMAN_ENSG000000128573
==== Molecular Function ====


RAT_1559697
===== 1)  transcription factor activity (GO:0003700) DONE =====


CHICK_769935
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.


DANRE_ZDB-GENE-041203-2
===== 2)  protein homodimerization activity (GO:0042803) DONE  =====


HUMAN_ENSG00000137166
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:


RAT_1311386
RAT_1562112
 
DANRE_ZDB-GENE-040426-1338
 
HUMAN_ENSG00000114861
 
RAT_1308669
 
CHICK_416092


because of positive experimental annotations to
because of positive experimental annotations to
Line 43: Line 36:
MOUSE_MGI:1891436
MOUSE_MGI:1891436


MOUSE_MGI:2148705
===== 3)  sequence specific DNA binding (GO:43565) DONE  =====


MOUSE_MGI:1921373
Up-propagation to common ancestor node AN588, down-propagation to the many Ref Genome proteins (see GAF) because of positive experimental annotations to


MOUSE_MGI:1914004
HUMAN_ENSG000000160973


===== 2)  transcription factor activity (GO:0003700) =====
MOUSE_MGI:1347465


Up-propagation to common ancestor node AN114, down-propagation to the following Ref Genome proteins:
MOUSE_MGI:1096329


RAT_1309196
DANRE_ZDB-GENE-000616-15


CHICK_421769
and more.


DANRE_ZDB-GENE-990708-6


CHICK_374231
==== Cellular Component:  ====


DANRE_ZDBJ-GENE-061013-59
===== 1)  nucleus (GO:0005634) DONE =====


DANRE_ENSDARG00000061549
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_1561201
No bacterial species are in this family, so erroneous annotation to 'nucleus' for bacteria is not a concern here.


CHICK_428703
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.'


HUMAN_ENSG00000204060


MOUSE_MGI:2676586
===== 2)  activin complex (GO:0032444) DONE =====


RAT_1595858
Up-propagation to common ancestor node AN597 down-propagation to:


DANRE_ENSDARG00000024619
RAT_1311275


DANRE_ENSDARG00000055792
because of positive experimental annotations to


DANRE_ZDB-GENE-050116-1
HUMAN_ENSG00000160973


because of positive experimental annotations to
MOUSE_MGI:1347465


HUMAN_ENSG00000118689
==== Biological Process:  ====


MOUSE_MGI:1890081
===== 1)  negative regulation of cell proliferation (GO:0008285) DONE =====


HUMAN_ENSG00000150907
Up-propagation to common ancestor node AN175, down-propagation to the following Ref Genome proteins:


MOUSE-MGI:1890077
RAT_1561201


RAT_620283
because of positive experimental annotations to


HUMAN_ENSG00000184481
HUMAN_ENSG00000184481
Line 97: Line 88:
MOUSE_MGI:1891915
MOUSE_MGI:1891915


==== Cellular Component:  ====
===== 2)  negative regulation of cell proliferation (GO:0008285) DONE  =====
 
===== 1)  nucleus (GO:0005634) =====
 
Up-propagation to common ancestor node AN20, down-propagation to the following Ref Genome proteins:


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


RAT_1562112
RAT_1562112


HUMAN_ENSG000000128573
because of positive experimental annotations to


RAT_1559697
HUMAN_ENSG00000049768


CHICK_769935
MOUSE_MGI:1891436


DANRE_ZDB-GENE-041203-2
===== 3) Immune response-related annotations: DONE =====


HUMAN_ENSG00000137166
    * 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)


RAT_1311386
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:


DANRE_ZDB-GENE-040426-1338
RAT_1562112
 
RAT_1308669
 
CHICK_416092


because of positive experimental annotations to
because of positive experimental annotations to
Line 128: Line 118:
HUMAN_ENSG00000049768
HUMAN_ENSG00000049768


MOUSE_MGI:1891436
MOUSE_MGI:1891436  


MOUSE_MGI:1914004
===== 4)  negative regulation of cell proliferation (GO:0008285) DONE  =====


HUMAN_ENSG00000114861 (annotated to nucleolus)
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF)


===== 2)  nucleus (GO:0005634) =====
because of positive experimental annotations to


Up-propagation to common ancestor node AN114, down-propagation to the following Ref Genome proteins:
HUMAN_ENSG00000184481
 
CHICK_421769
 
DANRE_ZDB-GENE-990708-6
 
CHICK_374231
 
DANRE_ZDBJ-GENE-061013-59
 
DANRE_ENSDARG00000061549


MOUSE_MGI:1891915
MOUSE_MGI:1891915


CHICK_428703
DROME_FBgn0038197
 
HUMAN_ENSG00000204060
 
RAT_1595858
 
DANRE_ENSDARG00000024619


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
===== 6) determination of left/right symmetry (GO:0007368) DONE =====
 
RAT_1561201
 
MOUSE_MGI:2676586
 
==== Biological Process:  ====


===== 1)  Immune response-related annotations: =====
Up-propagation to common ancestor node AN588, down-propagation to


* negative regulation of interferon-gamma production (GO:0032689)
HUMAN_ENSG00000160973
* 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_1311275
 
RAT_1561201


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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