Annotation Conf. Call, April 28, 2015

From GO Wiki
Revision as of 11:38, 12 May 2015 by Vanaukenk (talk | contribs) (Discussion)

Jump to: navigation, search


Agenda

Curation Consistency exercise

http://www.ncbi.nlm.nih.gov/pubmed/?term=24349431

Please send your annotations to MGI (David Hill)

Results

11 groups submitted 155 annotations: 3 mgi, Tair, wormbase, zfin, sgd, pombase, UCL, dictybase, GOA

Discussion

  • Cystin annotation to GO:0043433 negative regulation of sequence-specific DNA binding transcription factor activity Both cystin and necdin are able to activate transcription from the Myc P1 promoter above basal levels in vitro (see Figure 6C), although necdin activates to a greater degree than cystin. However, when cystin and necdin are expressed together, there is an antagonist effect on Myc transcription: Myc P1 promoter activity is lower than with necdin alone. The mechanism for this regulation is not demonstrated in this experiment; they did not show that cystin is specifically negatively regulating the DNA binding transcription factor activity of necdin. But the definition of GO:00043433: Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription, implies that it negatively regulates the totality of transcription not just the DNA binding part. So this term, as defined, would be fine to annotate cystin.
  • Is cystin regulating necdin? There is no evidence to show that cystin is regulating necdin - What would constitute evidence for this? The paper does show physical interaction between the two proteins and an effect on activity when co-transfected. So we can't put necdin as the regulation target of cystin. How would you capture the fact that cystin has the antagonist effect when necdin is present but it has the opposite role when it is acting alone? Would you use the evidence code or Col-16?
  • Would you use IGI as the evidence for how cystin interacts with necdin? Is cotransfection considered IGI? Both Rama and Midori thought this was not IGI based on current definition. Ruth, Rebecca and Rachael felt this would be IGI. Kimberly - I had originally used the IDA evidence code for the co-transfection experiment, but it seems that what we are really trying to capture with annotating this experiment is a functional interaction between two gene products. Although the type of experiment differs from traditional genetic experiments using multiply mutant strains, the conclusion is similar: these gene products functionally interact, even if we don't know the exact mechanism. The IGI evidence code therefore seems more appropriate to me now.
    • Reason for use of IGI: 2 cDNA constructs (cystin and necdin) transfected into a cell line, the effect is only seen when both constructs are present, therefore the use of IGI code enables the cystin to be annotated to negative reg of transcription (child term), and the addition of the necdin protein ID in the WITH field (the reciprocal annotation would not be created).
    • Reason against use of IGI: When only one of these genes is transfected into the cells the annotations created (pos reg of transcription, child term) are supported by the IDA evidence code not the IMP evidence code. The GOC documentation on IGI states: Includes any combination of alterations in the sequence (mutation) or expression of more than one gene/gene product.
    • Reason for using Col-16: The evidence code for the single transfection is IDA, therefore the IGI code can’t be used. Using Col-16 enables this information to be captured.
    • Reasons against using Col-16: There is no suitable relationship available to capture this data. There would be a lack of consistency in the application of evidence codes, e.g. If mutant and wt double transfectants were used then the IGI evidence code would be applied, and there would be information in the WITH field. Where as double wt transfectants would have no information in the WITH field.
  • The 'NLS bearing...' annotation is wrong- it is for proteins that can bind to NLS signals and import them into the nucleus
  • Chromatin- is not just histones and DNA. Should Txn factors be annotated to chromatin? Would you make a CC annotation to chromatin over a MF annotation to chromatin binding when you have ChiP evidence? Karen mentioned that in the paper she worked on with the Norway folks they decided all ChiP experiments should be CC. David mentioned that the way he decides between the two is : When you are binding chromatin you are not part of the chromatin. Is txn factor part of chromatin? We need to resolve this issue at the next GOC meeting (Midori has some rules, so does David). We will collect some use cases and present it at the GOC meeting. What should be included in the definition of chromatin?
    • DNA
    • RNA
    • histones
    • histone modifying complexes?
    • re-modeling complexes?
    • transcription factors?
  • RNA pol II binding- this is redundant with RNA Pol II txn factor complex annotation. Is there a link between the two? This is not always true, so no.
  • annotating to chromtin binding and putting Myc1 in col-16 is not right. It is upstream.
  • Use of IC evidence code? Most people have been using IDA when protein binding and transcription experiments are all in one paper. Use IC with GO_REF only evidence is from multiple papers
  • DNA binding annotation for cystin: Authors did not purify the protein (used nuclear extract) plus the protein doesn't have any DNA binding domain. So the DNA binding experiment can be indirect. It is okay to be strict and not make this annotation if the curator is not comfortable. We should be able to write why we decided to not make this annotation and make this comment public
  • BP and MF annotations using core promoter vs core promoter proximal region vs regulatory region - pick the term based on your confidence. Would it be possible to provide more guidelines for this in the GO term definitions?
  • annotating the standard marker proteins to the CC terms is not appropriate. They are controls to show that the cellular component includes the appropriate proteins, therefore capture of this information is circular. We need to document this practice.

Annotation Summary

Gene Term ID # of Annotations Evidence Code Summary 'With' field Summary Extension Summary
Biological Process Annotations
cystin negative regulation of transcription from RNA polymerase II promoter GO:0000122 4/11 IDA-3;IGI-1 necdin for the IGI annotation negatively_regulates-o-has-input Myc)(has_regulation_target Myc,occurs_in(mouse kidney epithelial cells - mIMCD-3))(has_regulation_target Myc)(has_direct_input necdin)
cystin regulation of transcription, DNA-templated GO:0006355 1/11 IDA
necdin regulation of transcription, DNA-templated GO:0006355 1/11 IDA
necdin positive regulation of transcription, DNA-templated GO:0045893 1/11 IDA (has_regulation_target Myc)
cystin positive regulation of transcription, DNA-templated GO:0045893 1/11 IDA (has_regulation_target Myc)
cystin negative regulation of transcription, DNA-templated GO:0045892 1/11 IDA (has_regulation_target Myc)
cystin regulation of transcription from RNA pol II promoter GO:0006357 2/11 IDA (has_regulation_target Myc)
necdin regulation of transcription from RNA pol II promoter GO:0006357 2/11 IDA (has_regulation_target Myc)
cystin NLS-bearing protein import into nucleus GO:0006607 1/11 IMP
cystin positive regulation of gene expression GO:0010628 1/11 IDA (has_regulation_target Myc)
necdin positive regulation of gene expression GO:0010628 1/11 IDA (has_regulation_target Myc)
cystin positive regulation of transcription from RNA polymerase II promoter GO:0045944 9/11 IDA;IGI-1 necdin for the IGI annotation (has_regulation_target Myc; 5 annotations)(occurs_in(mouse kidney epithelial cells - mIMCD-3; 1 annotation)(in_presence_of Myc; 1 annotation)(occurs_in 'kidney collecting duct cell; 1 annotation)
necdin positive regulation of transcription from RNA polymerase II promoter GO:0045944 8/11 IDA;IGI-1;IMP-1 cystin for the IGI annotation (has_regulation_target Myc; 5 annotations)(occurs_in(mouse kidney epithelial cells - mIMCD-3; 1 annotation)(in_presence_of Myc; 1 annotation)
cystin negative regulation of sequence-specific DNA binding transcription factor activity GO:0043433 4/11 IDA-1;IGI-1;IDA or IPI-1 necdin for the IGI (has_regulation_target necdin; 4 annotations)(occurs_in(mouse kidney epithelial cells - mIMCD-3; 1 annotation)(has_regulation_target+Myc; 1 annotation)
Cellular Component Annotations
cystin chromatin GO:0000785 1/11 IDA (coincident_with('GN box' or Myc P1 promoter' SO:new)
necdin chromatin GO:0000785 1/11 IDA (coincident_with('GN box' or Myc P1 promoter' SO:new)
cystin nuclear chromatin GO:0000977 1/11 IDA
necdin nuclear chromatin GO:0000977 1/11 IDA
cystin nucleus GO:0005634 11/11 IDA (part_of 'kidney inner medula collecting duct epithelial cell'; 1 annotation)(requires_sequence_feature NLS1; 1 annotation)(part_of mouse kidney epithelial cells - mIMCD-3; 1 annotation)(part_of CL:0002518 kidney epithelial cells; 1 annotation)(part_of 'kidney collecting duct cell; 1 annotation)(part_of+inner medulla collecting duct)
necdin nucleus GO:0005634 10/11 IDA (part_of 'kidney inner medula collecting duct epithelial cell'; 1 annotation)(requires_sequence_feature NLS1; 1 annotation)(part_of mouse kidney epithelial cells - mIMCD-3; 1 annotation)(part_of CL:0002518 kidney epithelial cells; 1 annotation)(part_of 'kidney collecting duct cell; 1 annotation)(part_of+inner medulla collecting duct)
necdin cytoplasm GO:0005737 7/11 IDA (part_of 'kidney inner medula collecting duct epithelial cell'; 1 annotation)(part_of mouse kidney epithelial cells - mIMCD-3; 1 annotation)(part_of 'kidney collecting duct cell; 1 annotation)
cystin cytoplasm GO:0005737 7/11 IDA (part_of 'kidney inner medula collecting duct epithelial cell'; 1 annotation)(part_of mouse kidney epithelial cells - mIMCD-3; 1 annotation)(requires_sequence_feature G2A)(part_of+inner medulla collecting duct)
cystin cytosol GO:0005829 5/11 IDA (part_of 'kidney inner medula collecting duct epithelial cell'; 1 annotation)(part_of mouse kidney epithelial cells - mIMCD-3; 1 annotation)(part_of 'kidney collecting duct cell; 1 annotation)
cystin plasma membrane GO:0005886 1/11 IDA
cystin membrane GO:0016020 10/11 IDA (part_of CL:0002518 kidney epithelial cells; 1 annotation)(part_of 'kidney inner medula collecting duct epithelial cell'; 1 annotation)(part_of mouse kidney epithelial cells - mIMCD-3; 1 annotation)(part_of 'kidney collecting duct cell; 1 annotation)(part_of+inner medulla collecting duct)
cystin RNA polymerase II transcription factor complex GO:0090575 3/11 IDA-2;IC-1 (part_of mouse kidney epithelial cells - mIMCD-3; 1 annotation)
necdin RNA polymerase II transcription factor complex GO:0090575 3/11 IDA-2;IC-1 (part_of mouse kidney epithelial cells - mIMCD-3; 1 annotation)
Molecular Function Annotations
necdin protein binding GO:0005515 8/11 IPI cystin-4 annotations (requires_sequence_feature aa 71 to 305; 1 annotation)
cystin protein binding GO:0005515 8/11 IPI necdin-4 annotations (requires_sequence_feature aa 71 to 305; 1 annotation)
necdin protein C-terminus binding GO:0008022 2/11 IPI cystin (requires_sequence_feature aa 71 to 305; 1 annotation)
cystin RNA polymerase II transcription factor binding GO:0001085 2/11 IPI necdin
cystin RNA polymerase II activating transcription factor binding GO:0001102 2/11 IPI necdin
necdin RNA polymerase II activating transcription factor binding GO:0001102 1/11 IPI cystin
necdin RNA polymerase II repressing transcription factor binding GO:0001103 1/11 IPI cystin
cystin chromatin binding GO:0003682 3/11 IDA has_input (Myc,promoter ; SO:0000167; 1 annotation)(has_direct_input Myc P1 promoter|occurs_in(mouse kidney epithelial cells - mIMCD-3)
necdin chromatin binding GO:0003682 3/11 IDA has_input (Myc,promoter ; SO:0000167; 1 annotation)(has_direct_input Myc P1 promoter|occurs_in(mouse kidney epithelial cells - mIMCD-3)
necdin sequence specific dna binding GO:0043565 1/11 IDA
cystin sequence specific dna binding GO:0043565 1/11 IDA
cystin transcription regulatory region sequence-specific DNA binding GO:0000976 1/11 IDA occurs_in mouse kidney epithelial cells - mIMCD-3)
necdin transcription regulatory region sequence-specific DNA binding GO:0000976 1/11 IDA occurs_in mouse kidney epithelial cells - mIMCD-3)
cystin RNA polymerase II regulatory region sequence-specific DNA binding GO:0000977 1/11 IDA occurs_in mouse kidney epithelial cells - mIMCD-3)
necdin RNA polymerase II regulatory region sequence-specific DNA binding GO:0000977 1/11 IDA occurs_in mouse kidney epithelial cells - mIMCD-3)
necdin RNA polymerase II core promoter sequence-specific DNA binding GO:0000979 1/11 IMP (has_direct_input+Myc)
cystin RNA polymerase II core promoter sequence-specific DNA binding GO:0000979 1/11 IMP (has_direct_input+Myc)
necdin RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000978 3/11 IDA (has_direct_input Myc; 1 annotation)(coincident_with 'GN box' or Myc P1 promoter' SO:new)
cystin RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000978 3/11 IDA (has_direct_input Myc; 1 annotation)(coincident_with 'GN box' or Myc P1 promoter' SO:new)
cystin sequence-specific DNA binding transcription factor activity GO:0003700 1/11 IPI (has_regulation_target Myc)
necdin sequence-specific DNA binding transcription factor activity GO:0003700 1/11 IPI (has_regulation_target Myc)
necdin RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription GO:0001077 2/11 IDA (has_regulation_target Myc)
cystin RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription GO:0001077 2/11 IDA (has_regulation_target Myc)
cystin RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription GO:0001191 1/11 IDA regulates-o-has-input Myc)
cystin RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription GO:0001227 1/11 IDA(IC?) (has_input Myc,in_presence_of necdin)
cystin RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription GO:0001228 1/11 IDA(IC?) (has_input Myc)
necdin RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription GO:0001228 1/11 IDA(IC?) (has_input Myc)
Other Genes
Trp53 protein binding GO:0005515 1/11 IPI Large T antigen
Cenpa nucleus GO:0005634 1/11 IDA
Capn2 cytosol GO:0005829 1/11 IDA
Cdh3 membrane GO:0016020 1/11 IDA