The Gaggle. Connect R to Firefox and assorted Java programs. Paul Shannon. Institute for Systems Biology & Seattle Biomedical Research Institute
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1 The Gaggle Connect R to Firefox and assorted Java programs Paul Shannon Institute for Systems Biology & Seattle Biomedical Research Institute
2 Overview Metaphors: goose, gaggle, boss, broadcast Four data types: namelist, matrix, network, hash map Semantic flexibility: the low road to data integration Firegoose
3 Motivating Example Identify up-regulated genes in R Broadcast Entrez GeneIDs to Firefox In Firefox, send them to EMBL STRING to explore for protein associations Broadcast expanded list and network back to R
4 Cytokine time course Locally released cytokines contribute to beta cell dysfunction and apoptosis in Type 1 diabetes. In vitro exposure of insulin producing INS 1E cells to the cytokines interleukin (IL) 1beta + interferon (IFN) gamma leads to a significant increase in apoptosis. To characterize the genetic networks implicated in beta cell dysfunction and apoptosis, we performed a time course analysis using the Affymetrix RG U34A microarry. INS 1E cells were exposed in duplicate to IL 1beta + IFN gamma for six different time points (1, 2, 4, 8, 12, and 24 h).
5 First Step, Always Start the Gaggle Boss using Java Web Start: This, and other related web start links, may be found on the workshop web page:
6 In R > library (gaggle) > gaggleinit () > m = read.table ('matrix.tsv', sep='\t') > rows = which (apply (m, 1, function (row) IQR (row) > 5)) > genes = row.names (m) [rows] > genes [1] "3122" "3934" "4599" "4843" "715 > geese () [1] "Network" "Firegoose" "DMV" "R-05 > settargetgoose ( Firegoose ) > broadcast (genes)
7 In Firefox: send to STRING
8 Find associations in STRING
9 Expand associations in STRING
10 Evidence in STRING
11 PubMed Abstracts from STRING
12 Broadcast network members back to R namelist ready, length 24 > from.string = getnamelist () > from.string [1] "ENSP " "ENSP " "ENSP " "ENSP " [5] "ENSP " "ENSP " "ENSP " "ENSP " [9] "ENSP " "ENSP " "ENSP " "ENSP " [13] "ENSP " "ENSP " "ENSP " "ENSP " [17] "ENSP " "ENSP " "ENSP " "ENSP " [21] "ENSP " "ENSP " "ENSP " "ENSP "
13 A Name Translation Goose Launch with Java Web Start Broadcast from Firefox/STRING to this goose Set up this goose to automatically broadcast translated names to R A good collection of these translators can solve many of the identifier problem bioinformaticians face
14 Name Translation Goose: Setup Firefox
15 Name Translation Goose In Action
16 Back in R > from.string = getnamelist () > from.string [1] "3122" "3108" "1514" "ENSP " [5] "3112" "7057" "ENSP " "912" [9] "857" "9722" "4843" "8434" [13] "3934" "7078" "4318" "3109" [17] "3125" "3123" "4846" "207" [21] "4599" "960" "4842" "972 > length (from.string) [1] 24 > length (intersect (from.string, rownames (m))) # suggested by STRING, in our data [1] 13 > new.genes = setdiff (intersect (from.string, rownames (m)), genes) > sapply (new.genes, function (row) IQR (m [row, ]))
17 Get STRING associations to R network ready, node count 24, edges: 60 > network = getnetwork () > edgedata (network) [1] $` ` $` `$edgeType [1] "embl string" $` `$`embl string url` [1] " 732&node2=312768" $` `$`combined association score` [1] > browseurl (edgedata (network)[[1]][[2]])
18 STRING evidence from R: browseurl (edgedata (network)[[1]][[2]])
19 An Expression Movie Overlay (and animate) time-course expression levels on network derived from STRING Requires two new geese: DMV and Cytosape Cytoscape 2.5 almost ready; but using ancient Cytoscape 1.2 for now Begin by broadcasting matrix from R to DMV
20 An Expression Movie, cont. Start DMV: Start Cytoscape:
21 An Expression Movie, cont. > geese () [1] "Human-01" "DMV-01" [3] "Network" "Firegoose" [5] "STRING-GeneID, Human, v7.0 "R-05 > settargetgoose ( DMV-01 ) # or stg (2) > broadcast (m, ratios ) > settargetgoose ( Human-01 ) # or stg (1) > broadcast (network) > stg (2); showgoose () # bring DMV to the front
22 An Expression Movie, cont.
23 An Expression Movie, cont. 4 Hours
24 An Expression Movie, cont. 8 Hours
25 Future Plans GWAP: the gaggle web application Add a genome browser (Apollo from flybase?) Support Cytoscape 2.5 Embedded gaggle markup at bioinformatics websites Systems Biology Markup Language (SBML) Better integration of MeV (Multi-experiment viewer) Socket communication to complement Java RMI
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