Annotation Conf. Call 2016-10-25

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Agenda

Meetings

Next GOC Meeting - USC, Los Angeles, CA, November 4-6, 2016

  • Link to a registration form is now available for the USC Meeting on the Meeting Logistics Page.
  • Register for meeting and dinner, just dinner, just meeting.
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  • Draft Agenda - please review

Discussion of Outstanding github Tickets

Annotation Consistency Exercise

Abstract AIM:To elucidate the sequential transfer of iron amongst ferritin, transferrin and transferrin receptor under various iron status conditions. METHODS:Incorporation of 59Fe into mucosal and luminal proteins was carried out in control WKY rats. The sequential transfer of iron amongst ferritin, transferrin and transferrin receptor was carried out in iron deficient, control and iron overloaded rats. The duodenal proteins were subjected to immunoprecipitation and quantitation by specific ELISA and in situ localization by microautoradiography and immunohistochemistry in tandem duodenal sections. Human duodenal biopsy (n = 36) collected from subjects with differing iron status were also stained for these proteins. RESULTS:Ferritin was identified as the major protein that incorporated iron in a time-dependent manner in the duodenal mucosa. The concentration of mucosal ferritin was significantly higher in the iron excess group compared to control, iron deficient groups (731.5 +/- 191.96 vs 308.3 +/- 123.36, 731.5 +/- 191.96 vs 256.0 +/- 1.19, P < 0.005), while that of luminal transferrin which was significantly higher than the mucosal did not differ among the groups (10.9 +/- 7.6 vs 0.87 +/- 0.79, 11.1 +/- 10.3 vs 0.80 +/- 1.20, 6.8 +/- 4.7 vs 0.61 +/- 0.63, P < 0.001). In situ grading of proteins and iron, and their superimposition, suggested the occurrence of a sequential transfer of iron. This was demonstrated to occur through the initial binding of iron to luminal transferrin then to absorptive cell surface transferrin receptors. The staining intensity of these proteins varied according to the iron nutrition in humans, with intense staining of transferrin receptor observed in iron deficient subjects. CONCLUSION:It is concluded that the intestine takes up iron through a sequential transfer involving interaction of luminal transferrin, transferrin-transferrin receptor and ferritin.

Discussion Points

  1. What can be done with ferritin annotations, since a specific subunit was non identified in the paper?
  2. Should colocalization (IEP) data be used for biological process annotations?
  3. If an iron transport annotation is made, does an iron homeostasis annotation impart any additional information?
  4. Is "intestinal absorption" too broad? Should an intestinal iron absorption term be requested?

Accompanying LEGO Model

Annotations

Gene Symbol, Gene Name GO term/ID Evidence Code Annotation Source Annotation Extension Comment
Biological Process
ferritin iron ion transport GO:0006826 IDA FB, Tair Which ferritin subunit?
Tf, transferrin iron ion transport GO:0006826 IDA FB, Tair transport is inferred from radioactive Fe sequential colocalizing with location of each of the proteins in different parts of the duodenum
Tfrc, transferrin receptor iron ion transport GO:0006826 IDA FB, Tair Tfrc or Tfr2?
Tf, transferrin ferric iron transport GO:0015682 IDA RGD
ferritin ferric ion import GO:0033216  ? SGD occurs_in UBERON:0000320 duodenal mucosa
Tf, transferrin ferric ion import GO:0033216  ? SGD occurs_in UBERON:0000320 duodenal mucosa
Tf, transferrin GO:0098706 -ferric iron import across plasma membrane IEP WB
Tfrc, transferrin receptor GO:0098706 -ferric iron import across plasma membrane IEP WB
ferritin iron ion homeostasis GO:0055072 IDA FB Which ferritin subunit?
Tf, transferrin iron ion homeostasis GO:0055072 IDA FB transport is inferred from radioactive Fe sequential colocalizing with location of each of the proteins in different parts of the duodenum
Tfrc, transferrin receptor iron ion homeostasis GO:0055072 IDA FB
ferritin, Fth1, Ftl1 GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0016512) lumen of duodenum
Tf, transferrin GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0016512)lumen of duodenum
Tfrc, transferrin receptor GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0002114) duodenum
Tf, transferrin GO:0050892 - intestinal absorption IEP WB has_input(ChEBI:29034) Maybe request "intestinal iron ion absorption".
Tfrc, transferrin receptor GO:0050892 - intestinal absorption IEP WB has_input(ChEBI:29034)
Tf, transferrin response to iron ion GO:0010039 IEP RGD movement between compartments dependent on iron level in diet
Tfrc, transferrin receptor response to iron ion GO:0010039 IEP RGD
human ferritin, FTH1 (UniProtKB:P02794), FTL (UniProtKB:P02792) GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0002114) duodenum
human TF (UniProtKB:P02787) GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0002114) duodenum
human TFRC (UniProtKB:P02786) GO:0060586 - multicellular organismal iron ion homeostasis IEP WB occurs_in(UBERON:0002114) duodenum
Cellular Component
Tf, transferrin cell tip GO:0051286 IDA RGD Figure 5 - ID, 15 min; text description
Tfrc, transferrin receptor cell surface GO:0009986 IDA RGD Figure 5; text description
Tfrc, transferrin receptor GO:0031528 - microvillus membrane IDA WB
Tf, transferrin, Fth1, Ftl1, ferritin GO:0005615 - extracellular space IDA WB
Molecular Function
Fth1, Ftl1, ferritin iron ion binding, GO:0005506 IDA FB, Tair, WB occurs_in UBERON:0000320 duodenal mucosa Which ferritin subunit?
Tf, transferrin iron ion binding, GO:0005506 IDA FB, Tair, WB occurs_in UBERON:0000320 duodenal mucosa
Tf, transferrin ferric iron binding GO:0008199 IDA RGD, SGD
ferritin ferric iron binding GO:0008199 IDA SGD
Tfrc, transferrin receptor GO:0004998 - transferrin receptor activity IEP WB occurs_in(UBERON:0008346) duodenal epithelium IEP for MF annotation???

Minutes

  • On call: Alice, Barbara, Edith, FlyBase, Kimberly, Li, Midori, Olivia, Paola, Paul, Penelope, Petra, Sabrina, Sage, Stacia, Stan, Tanya, Val