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 ====
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 ====


Propagation:
===== 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


===== 1)  transcription factor activity (GO:0003700) =====
DANRE_ZDB-GENE-000616-15


Up-propagation to common ancestor node AN0, the root node, down-propagation to the following Ref Genome proteins:
and more.


based on many experimental annotations, from yeast to human, that map up to the root node.


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


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


Up-propagation to common ancestor node AN20, 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.


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.'


RAT_1562112


HUMAN_ENSG000000128573
===== 2)  activin complex (GO:0032444) DONE =====


RAT_1559697
Up-propagation to common ancestor node AN597 down-propagation to:


CHICK_769935
RAT_1311275


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


HUMAN_ENSG00000137166
HUMAN_ENSG00000160973


RAT_1311386
MOUSE_MGI:1347465


DANRE_ZDB-GENE-040426-1338
==== Biological Process:  ====


RAT_1308669
===== 1)  negative regulation of cell proliferation (GO:0008285) DONE =====


CHICK_416092
Up-propagation to common ancestor node AN175, down-propagation to the following Ref Genome proteins:
 
RAT_1561201


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


HUMAN_ENSG00000049768
HUMAN_ENSG00000184481


MOUSE_MGI:1891436
MOUSE_MGI:1891915


MOUSE_MGI:1914004
===== 2)  negative regulation of cell proliferation (GO:0008285) DONE  =====


HUMAN_ENSG00000114861 (annotated to nucleolus)
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:


===== 2)  nucleus (GO:0005634) =====
RAT_1562112


Up-propagation to common ancestor node AN114, down-propagation to the following Ref Genome proteins:
because of positive experimental annotations to


CHICK_421769
HUMAN_ENSG00000049768


DANRE_ZDB-GENE-990708-6
MOUSE_MGI:1891436


CHICK_374231
===== 3) Immune response-related annotations: DONE =====


DANRE_ZDBJ-GENE-061013-59
    * 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)


DANRE_ENSDARG00000061549
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:


MOUSE_MGI:1891915
RAT_1562112


CHICK_428703
because of positive experimental annotations to


HUMAN_ENSG00000204060
HUMAN_ENSG00000049768


RAT_1595858
MOUSE_MGI:1891436


DANRE_ENSDARG00000024619
===== 4)  negative regulation of cell proliferation (GO:0008285) DONE  =====


DANRE_ENSDARG00000055792
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF)
 
DANRE_ZDB-GENE-050116-1


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


HUMAN_ENSG00000118689
HUMAN_ENSG00000184481


MOUSE_MGI:1890081
MOUSE_MGI:1891915


RAT_1309196
DROME_FBgn0038197


HUMAN_ENSG000000150907
===== 5)  insulin receptor signaling pathway (GO:0008286) DONE  =====


MOUSE_MGI:1890077
Up-propagation to common ancestor node AN111, down-propagation to several Ref Genome proteins (see GAF)


RAT_620283
because of positive experimental annotations to


HUMAN_ENSG00000184481
HUMAN_ENSG00000184481


RAT_1561201
MOUSE_MGI:1890077


MOUSE_MGI:2676586
DROME_FBgn0038197


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


===== 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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