Annotation Conf. Call September 24th, 2013
Annotation extension exercises
Paper 1: PMID 17620096 (Title: Human S100A15 splice variants are differentially expressed in inflammatory skin diseases and regulated through Th1 cytokines and calcium.)
http://www.ncbi.nlm.nih.gov/pubmed/17620096
Annotation Extension to be discussed for the cytoplasm annotation for S100A14.
DB (Col 2) | GO ID (Col 5) | ev.code | Reference (Col 6) | Extension (Col 16) |
---|---|---|---|---|
S100A14, Q9HCY8 | GO:0005737 (cytoplasm) | IDA | PMID:17620096 | part_of: CL:0000362 (epidermal cell) |
Evidence is from Figure 3 and text on page 687: "hS100A15 is predominantly expressed in the epidermis of psoriatic and atopic skin
Because psoriasis and atopic eczema are characterized by morphological changes in both dermis and epidermis, we investigated the distribution of the hS100A15 transcripts in normal and diseased skin by in situ hybridization. Both S100A15 isoforms were detected mainly in the epidermis of normal and inflamed skin and showed a similar distribu- tion pattern. In line with RT-PCR analysis, the expression of S100A15-S was less pronounced than S100A15-L. Within the faint staining of healthy skin, hS100A15-L transcripts were present in the cytoplasm of the basal epidermal layer (Fig. 3, arrow), whereas the differentiated epidermal layers showed weak probe reactivity to hS100A15-L. "
Paper 2: PMID 9799565 (Title: Role of human CYP4F2 in hepatic catabolism of the proinflammatory agent leukotriene B4.)
http://www.ncbi.nlm.nih.gov/pubmed/9799565
Annotation Extension to be discussed for the leukotriene-B4 20-monooxygenase activity annotation for CYP4F2.
DB (Col 2) | GO ID (Col 5) | ev.code | Reference (Col 6) | Extension (Col 16) |
---|---|---|---|---|
CYP4F2, P78329 | GO:0050051 (leukotriene-B4 20-monooxygenase activity) | IDA | PMID:9799565 | occurs_in: UBERON:0002107 (liver) |
Evidence is from Table III
Paper 3: PMID 23437011 - This is a long paper, so only a few annotations will be discussed. (Title: The Caenorhabditis elegans JNK signaling pathway activates expression of stress response genes by derepressing the Fos/HDAC repressor complex.)
http://www.ncbi.nlm.nih.gov/pubmed/23437011
Annotation Extension to be discussed for KGB-1 phosphorylation of FOS-1
DB (Col 2) | GO ID (Col 5) | ev.code | Reference (Col 6) | Extension (Col 16) |
---|---|---|---|---|
WB:WBGene00002187 or UniProtKB:O44408 | GO:0004674 (protein serine/threonine kinase activity) | IDA | PMID:23437011 | has_direct_input: WB:WP:CE27375 or UniProtKB:G5EDK8 (FOS-1B in paper, the 331 amino acid isoform in WB and UniProtKB) |
Relevant text (not inclusive, i.e., there are other statements that also support the annotation):
As FOS-1A has previously been characterized as a regulator of anchor-cell invasion during nematode development [17], we focused our investigations on the FOS-1B form (hereafter referred to as FOS-1).
Figure 1. FOS-1 is phosphorylated by KGB-1.
We further generated three FOS-1 mutants that individually changed Thr-304, Thr-316, or Thr-318 to Ala and found that the FOS-1(T304A) mutation exhibited decreased phosphorylation by KGB-1 (Figure 1D, line 3 and Figure S2). These results suggest that T304 is a major site of phosphorylation.
To confirm that KGB-1 phosphorylates FOS-1 at the Thr-304 residue, we generated anti-phospho-FOS-1 antibodies that specifically recognize FOS-1 phosphorylated at Thr-304. Transfection with active KGB-1, but not with the kinase-negative mutant KGB-1 KN, resulted in strong reactivity of FOS-1 with this antibody (Figure 1D, lanes 1, 2). In contrast, we found that the FOS-1 (T304A) mutated form could not be detected by this antibody (Figure 1D, lane 3), confirming that it was specific for FOS-1 phosphorylated at Thr-304.
Note: The phosphorylation experiments reportedly rely on an activated form of KGB-1 (activated by another protein kinase, MEK-1) but there doesn't seem to be a control in the paper that definitively shows this. Therefore, I haven't added any additional information about the role of MEK-1. We could discuss this on the call.
Annotation Extension to be discussed for KGB-1 regulation of FOS-1 oligomerization
DB (Col 2) | GO ID (Col 5) | ev.code | Reference (Col 6) | Extension (Col 16) |
---|---|---|---|---|
WB:WBGene00002187 or UniProtKB:O44408 | GO:0032463 (negative regulation of protein homooligomerization) | IDA | PMID:23437011 | has_regulation_target: WB:WP:CE27375 or UniProtKB:G5EDK8 (FOS-1B in paper, the 331 amino acid isoform in WB and UniProtKB) |
Relevant text:
Indeed, GFP-FLAG-FOS-1 readily co-immunoprecipitated with T7-FOS-1 (Figure 1E, lanes 1, 2), indicating that the two proteins oligomerized, presumably as dimers.
Co-expression of active but not inactive KGB-1 resulted in reduced co-immunoprecipitation of T7-FOS-1 with GFP-FLAG-FOS-1 (Figure 1E, lanes 3, 4).
Annotation Extension to be discussed for FOS-1 regulation of kreg-1 and kreg-2 transcription