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 7: Line 18:
[http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO2OM/ORTHOMCL14416 PPOD/OrthoMCL link]
[http://ppod.princeton.edu/cgi-bin/ppod.cgi/GO2OM/ORTHOMCL14416 PPOD/OrthoMCL link]


==== 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.
 
===== 2)  protein homodimerization activity (GO:0042803) DONE =====
 
Up-propagation to common ancestor node AN27, down-propagation to the following Ref Genome proteins:


SourceForge notes:
RAT_1562112
DNA binding - human IDA, mouse ISS


Seq-spec and ds DNA binding - rat IDA - ISS to human and mouse?
because of positive experimental annotations to


TF activity - human IDA, Rat ISS - ISS to mouse?
HUMAN_ENSG00000049768


Transcription repressor activity - Rat IDA, mouse ISS - ISS to Human?
MOUSE_MGI:1891436


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


===== 1)  transcription factor activity (GO:0003700) =====
Up-propagation to common ancestor node AN588, down-propagation to the many Ref Genome proteins (see GAF) because of positive experimental annotations to


Up-propagation to common ancestor node AN24, down-propagation to the following Ref Genome proteins:
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
RAT_1562112


HUMAN_ENSG000000128573
because of positive experimental annotations to


RAT_1559697
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
because of positive experimental annotations to
Line 34: Line 118:
HUMAN_ENSG00000049768
HUMAN_ENSG00000049768


MOUSE_MGI:1891436
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:2148705
MOUSE_MGI:1890077


==== Cellular Component:  ====
DROME_FBgn0038197


SourceForge notes:
===== 6) determination of left/right symmetry (GO:0007368) DONE  =====


Nucleus (human, rat) - ISS to mouse?
Up-propagation to common ancestor node AN588, down-propagation to


Mouse has no component annotation
HUMAN_ENSG00000160973


==== Biological Process:  ====
RAT_1311275


SourceForge notes:
because of positive experimental annotations to
Both -ve and +ve regulation of transcription terms are present, but from
looking at papers this seems OK.


-ve regulation of transcription - rat IDA, mouse ISS - ISS to human?
MOUSE_MGI:1347465


+ve regulation of transcription human IDA, rat ISS - ISS to mouse?
DANRE_ZDB-GENE-000616-15


Thyroid gland development (human IMP, mouse IMP, rat ISS)
==== 7) ovarian follicle development (GO:0001541) DONE  =====


Hard palate development - human IMP, rat ISS - ISS to mouse?
Up-propagation to common ancestor node AN1048, down-propagation to


Soft palate development - human IMP, rat ISS - ISS to mouse?
RAT_1310041


cell migration - mouse IMP, rat ISS - ISS to human?
because of positive experimental annotations to


embryonic organ and hair follicle morphogenesis terms - Mouse IMP, rat ISS
MOUSE_MGI:1349428
- ISS to human?


thyroid hormone generation - mouse IMP, rat ISS - ISS to human?
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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