Panther ID:11829: Difference between revisions

From GO Wiki
Jump to navigation Jump to search
No edit summary
 
(29 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 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:
 
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.


SourceForge notes:
No bacterial species are in this family, so erroneous annotation to 'nucleus' for bacteria is not a concern here.
DNA binding - human IDA, mouse ISS
Seq-spec and ds DNA binding - rat IDA - ISS to human and mouse?


TF activity - human IDA, Rat ISS - ISS to mouse?
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.'
Transcription repressor activity - Rat IDA, mouse ISS - ISS to Human?


Propagation:


===== 1activity (GO:) =====
===== 2activin complex (GO:0032444) DONE =====


Up-propagation to common ancestor node AN, down-propagation to the following Ref Genome proteins:
Up-propagation to common ancestor node AN597 down-propagation to:


RAT_1311275


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


==== Cellular Component: ====
HUMAN_ENSG00000160973
 
MOUSE_MGI:1347465


==== Biological Process:  ====
==== 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]]
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