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Welcome to the wonderful world of our Objective 1, Here we would be trying to predict the Ubiquitination sites and factors involved in NF-kB pathway. To make your life easier (*insert evil laugh*), we would consider only the alternate (non-canonical) pathway.
Instead of randomly picking structures, we can make an informed choice. We would be using Cytoscape for the purposes of data mining.
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This plugin would help you be lazy. Just put in the search term and it will spew out a range of pubmed citations as well as draw a network for you while you have a sip of coffee.
The downside is it that it tries to be smart and screws up things at times (which is normal for any AI)
The other downside, specially in this scenario, is that it fails if there aren't any relevant pubmed citations.
This
KEGG
Vizmapper.
Using the results given by Agilent Literature Search as a start, go to Pathway Commons and restrict the search results to Humans and House Mouse.
All of the networks that I studied were related to Nature Pathway DB and Reactome. But I left all DBs checked, just in case.
Then I download the following files for NF-kB Alternate pathway.
http://www.pathwaycommons.org/pc/record2.do?id=517194
http://www.pathwaycommons.org/pc/record2.do?id=4927
http://www.pathwaycommons.org/pc/record2.do?id=101972
And the following specific to Ubiquitination:
http://www.pathwaycommons.org/pc/record2.do?id=539743
http://www.pathwaycommons.org/pc/record2.do?id=486233
http://www.pathwaycommons.org/pc/record2.do?id=501852
Now coming over to the overall CD8+ pathway, some interesting CPathIds are 7626297, 540883, 538611, 7695677, 7712414, 7655793 ... (I got bored). Just making a note of it at the moment. We might need them if we try to give a live example of Alzheimers or Parkinsons later. (Can't juggle with so many balls at the same time now). But of course, these can be mentioned as possible motifs in an intermediate paper.
RESULTSET:
Gene Set #
Gene Symbols: Alternative NF-kappaB pathway NCI_NATURE BTRC RELB NFKB1 NFKB2 MAP3K14 CHUK
Entrez Gene IDs: Alternative NF-kappaB pathway NCI_NATURE 5971 1147 8945 9020 4791 4790
Uniprot IDs: Alternative NF-kappaB pathway NCI_NATURE Q68D84 Q9Y297 Q99558 Q6GTX7 Q9BU75 O15111 B5MD49 A8K2D8 Q00653 Q92467 Q9UEI7 Q13132 D3DX67 Q5W0I4 Q5W142 Q04860 Q9NZC0 Q86V43 Q9Y213 P19838 O14666 Q01201 Q8IYN1 Q9H471 Q9H472 D3DR83 Q8N4X7
Analysing the network maps, point to the various CPathIDs to get the following observations:
1. using the CPATH ID 520728 in http://www.pathwaycommons.org/pc/record2.do?id=520728 gives us the Ubiquitination of p100 -> p52. There are no journal citations (apparently we chose a difficult {impossible??} topic).
2. using CPathID 531002 gives us ßTrCP/SCF ligase based ubiquitination. This is longer than #1 but has some citations. I think we can start from here.
3. Another interesting pathway is of 528166 which is around translocation of p52/RelB into nucleoplasm. Never found any articles that explained this. Not getting into this one.
4. The B Cell activation is done by 518782. No citations here either. But there are some other interesting binding points in the CD8 cycle.
Additionally looking at the KEGG pathway from http://www.kegg.jp/kegg-bin/show_pathway?hsa04064+8737, (look at the bottom for Osteclast Differentiation) we can see the Alternate NF-kB2 signalling pathway. We see the molecules of interest are:
LT-βR (4MXW and 1TNR),
TRAF2 (3M06, 3KNV, 1F3V),
LIGHT (4EN0, 4KG8, 4KGQ),
TRAF3 (no complete crystal structure found. may be something comes up during BLAST of partial str 1FLK, 1FLL),
NIK (4DN5, 4G3D, 4IDT, 4IDV).
The substrates would be:
IKKα (http://www.genome.jp/dbget-bin/www_bget?sp:O15111)
p52 (1A3Q, 2D96)
RelB (Uniprod ID: Q01201).
[Plus this entry, may be? http://www.kegg.jp/dbget-bin/www_bget?hsa:6387]
Browsing through other sub networks,
we can see KEGG details that http://www.kegg.jp/dbget-bin/www_bget?hsa:4791 gives
PFAM details that http://www.genome.jp/dbget-bin/www_bget?pfam:RHD gives
a link out to LinkDB that http://www.genome.jp/dbget-bin/get_linkdb?-t+pdb+pf:RHD provides us the interesting structures as:
1NFK, 1RAM (obsolete), 2RAM, 1SVC and 2V2T, 1LB6 3HCT 3HCS 1LB4 1LB5 3HCU 2ECI 2JMD.
need to weed out some of these in the next stage.
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I have attached some .png files for ref. But I have observed that Cytoscape renders the networks in different ways depending on the OS, Graphics Card, monitor size etc.
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