Ontology searches with RNA sequencing data of Saccharomyces cerevisiae wt/mutant cbf5.
This document will pull together the various annotations and results from the differential expression analyses and attempt to use them for gene ontology searches.
RNA sequencing of Saccharomyces cerevisiae wt/mutant cbf5.
This document performs the differential expression analyses of wt/mut CBF5 yeast strains. Depending on my mood, it may also include some comparisons against an external data set of upf1/2/3 mutant strains which I randomly found.
Genome annotation input
There are a few methods of importing annotation data into R. The following are two attempts, the second is currently being used in these analyses.
AnnotationHub: loading OrgDb
AnnotationHub is a newer service and has promise to be an excellent top-level resource for gathering annotation data.
Loading a TxDb
OrgDbs provide a set of links between different annotation resources, in the case of yeast that includes GO/KEGG/SGD IDs. We also want links between gene annotations and these gene IDs. The TxDb system provides this information.
Loading a genome
There is a non-zero chance we will want to use the actual genome sequence along with these annotations. The BSGenome packages provide that functionality.
Loading from biomart
A completely separate and competing annotation source is biomart.
Merging them into an OrganismDb
At this point we have multiple possible ways to mix and match these annotation data. Ideally I would like to put them all into a single format, organismDb is a good choice therefore.
Read a gff file
In contrast, it is possible to load most annotations of interest directly from the gff files used in the alignments.
Putting the pieces together
The following block sets up a master experiment containing one set of anontations and all the reads.
At this point, we should have everything necessary to play!
Perform simplified differential expression
My function all_pairwise() makes use of limma, deseq, edger, and implements a basic differential expression algorithm. Using it we should be able to compare/contrast the wt/mutant as well as different tools.
There is an important caveat for this data: There is exactly 1 batch and 4 replicates. Thus we need to make sure that the statistical models never attempt to include experimental batch (which is the default). Later, we will include the exogeneous data and make them batch against one another.
Do the comparison of only the wt/mutants
Do a similar comparison but including the exogeneous data
If I want to try including the exogeneous data, then I will need to make sure batch stays in the model and/or I will need to use batch-adjusted data and remove batch from the model. I should probably try both ways and see how they compare…
Also note that I combined upf1/upf2/upf3 into one condition called ‘nmd’.
Ontology searching is weird
Sadly, the authors of the various ontology tools I use (goseq/clusterprofiler/topgo/gostats/gprofiler) keep changing the input requirements and make it hard for me to keep up. Lets see how well I did.
Searching with goseq
I want to search the set of up/down genes using goseq, since they changed how they accept annotations, I am changing the goseq search to match the new methods. I think they will be better but am not yet certain.
de_genes <- s_p(get_sig_genes(table=our_tables$data[[1]], fc=1, p=0.05, column="limma_logfc", p_column="limma_adjp"))$result## Assuming the fold changes are on the log scale and so taking >< 0## After (adj)p filter, the up genes table has 1973 genes.## After (adj)p filter, the down genes table has 1069 genes.## Assuming the fold changes are on the log scale and so taking -1 * fc## After fold change filter, the up genes table has 451 genes.## After fold change filter, the down genes table has 352 genes.up_genes <- de_genes$up_genes
down_genes <- de_genes$down_genes
## There is a super important caveat before doing the ontology search
## The gff annotations I used for the alignments included a mix of transcripts and genes, which confuses the ontology searches
## Therefore I need to re-index the rows to use the canonical transcript IDs.
rownames(up_genes) <- up_genes$transcriptid
rownames(down_genes) <- down_genes$transcriptid
our_upgoseq <- s_p(hpgltools:::new_simple_goseq(de_genes=up_genes, go_db=sc_orgdb, length_db=sc_txdb))$result## Returning metadf.## Using Orgdb.## 'select()' returned 1:many mapping between keys and columns## Using manually entered categories.## Calculating the p-values...## 'select()' returned 1:1 mapping between keys and columns## simple_goseq(): Calculating q-values## Using GO.db to extract terms and categories.## simple_goseq(): Filling godata with terms, this is slow.## Testing that go categories are defined.## Removing undefined categories.## Gathering synonyms.## Gathering category definitions.## simple_goseq(): Making pvalue plots for the ontologies.
our_upgoseq$pvalue_plots$bpp_plot_over
our_upgoseq$pvalue_plots$mfp_plot_over
our_upgoseq$pvalue_plots$ccp_plot_over
our_downgoseq <- s_p(hpgltools:::new_simple_goseq(de_genes=down_genes, go_db=sc_orgdb, length_db=sc_txdb))$result## Returning metadf.## Using Orgdb.## 'select()' returned 1:many mapping between keys and columns## Using manually entered categories.## Calculating the p-values...## 'select()' returned 1:1 mapping between keys and columns## simple_goseq(): Calculating q-values## Using GO.db to extract terms and categories.## simple_goseq(): Filling godata with terms, this is slow.## Testing that go categories are defined.## Removing undefined categories.## Gathering synonyms.## Gathering category definitions.## simple_goseq(): Making pvalue plots for the ontologies.
our_downgoseq$pvalue_plots$bpp_plot_over
our_downgoseq$pvalue_plots$mfp_plot_over
our_downgoseq$pvalue_plots$ccp_plot_over
I separate out the running of the ontology search from writing it to excel so it does not re-print the graphs to the report.
our_upwritten <- hpgltools:::write_new_goseq_xlsx(our_upgoseq, file="excel/mutwtup_goseq.xlsx")
our_downwritten <- hpgltools:::write_new_goseq_xlsx(our_downgoseq, file="excel/mutwtdown_goseq.xlsx")Try gProfiler
up_gprofiler <- s_p(simple_gprofiler(de_genes=up_genes, species="scerevisiae"))$result## Performing g:Profiler GO search.## GO search found 108 hits.## Performing g:Profiler KEGG search.## KEGG search found 11 hits.## Performing g:Profiler reactome.db search.## Reactome search found 0 hits.## Performing g:Profiler miRNA search.## miRNA search found 0 hits.## Performing g:Profiler transcription-factor search.## transcription-factor search found 17 hits.## Performing g:Profiler corum search.## corum search found 0 hits.## Performing g:Profiler hp search.## hp search found 1 hits.up_gprofiler$plots$kegg_plot_over
up_gprofiler$plots$tf_plot_over
up_gprofiler$plots$bpp_plot_over
down_gprofiler <- s_p(simple_gprofiler(de_genes=down_genes, species="scerevisiae"))$result## Performing g:Profiler GO search.## GO search found 22 hits.## Performing g:Profiler KEGG search.## KEGG search found 7 hits.## Performing g:Profiler reactome.db search.## Reactome search found 0 hits.## Performing g:Profiler miRNA search.## miRNA search found 0 hits.## Performing g:Profiler transcription-factor search.## transcription-factor search found 1 hits.## Performing g:Profiler corum search.## corum search found 0 hits.## Performing g:Profiler hp search.## hp search found 1 hits.down_gprofiler$plots$kegg_plot_over
down_gprofiler$plots$tf_plot_over
down_gprofiler$plots$bpp_plot_over
Try KEGG
It has been quite a while since last I used KEGG in an efficient fashion, lets see what happens!
library(pathview)
try_species = kegg_get_orgn("Saccharomyces cerevisiae")
pathview_data = our_tables$data[[1]]
rownames(pathview_data) = make.names(pathview_data$transcriptid, unique=TRUE)
## If I read the yeast xml files correctly, they all follow the traditional chromosomal location naming scheme...
pathview_result = s_p(hpgl_pathview(pathview_data, species=try_species, filenames="name"))$result## ##############################################################################
## Pathview is an open source software package distributed under GNU General
## Public License version 3 (GPLv3). Details of GPLv3 is available at
## http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to
## formally cite the original Pathview paper (not just mention it) in publications
## or products. For details, do citation("pathview") within R.
##
## The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG
## license agreement (details at http://www.kegg.jp/kegg/legal.html).
## ################################################################################ Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00010._colored.png## Warning in file.rename(from = oldfile, to = newfile): cannot rename file
## 'sce00010._colored.png' to 'pathview/glycolysis_/_gluconeogenesis_colored.png', reason 'No
## such file or directory'## 1/114: Finished glycolysis_/_gluconeogenesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00020._colored.png## 2/114: Finished citrate_cycle_(tca_cycle)## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00030._colored.png## 3/114: Finished pentose_phosphate_pathway## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00040._colored.png## 4/114: Finished pentose_and_glucuronate_interconversions## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00051._colored.png## 5/114: Finished fructose_and_mannose_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00052._colored.png## 6/114: Finished galactose_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00061._colored.png## 7/114: Finished fatty_acid_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00062._colored.png## Info: some node width is different from others, and hence adjusted!## 8/114: Finished fatty_acid_elongation## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00071._colored.png## 9/114: Finished fatty_acid_degradation## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00072._colored.png## 10/114: Finished synthesis_and_degradation_of_ketone_bodies## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00100._colored.png## 11/114: Finished steroid_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00130._colored.png## 12/114: Finished ubiquinone_and_other_terpenoid-quinone_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00190._colored.png## Info: some node width is different from others, and hence adjusted!## 13/114: Finished oxidative_phosphorylation## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00220._colored.png## 14/114: Finished arginine_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00230._colored.png## 15/114: Finished purine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00240._colored.png## 16/114: Finished pyrimidine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00250._colored.png## 17/114: Finished alanine,_aspartate_and_glutamate_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00260._colored.png## 18/114: Finished glycine,_serine_and_threonine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00261._colored.png## 19/114: Finished monobactam_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00270._colored.png## 20/114: Finished cysteine_and_methionine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00280._colored.png## 21/114: Finished valine,_leucine_and_isoleucine_degradation## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00290._colored.png## 22/114: Finished valine,_leucine_and_isoleucine_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00300._colored.png## 23/114: Finished lysine_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00310._colored.png## 24/114: Finished lysine_degradation## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00330._colored.png## 25/114: Finished arginine_and_proline_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00332._colored.png## 26/114: Finished carbapenem_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00340._colored.png## 27/114: Finished histidine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00350._colored.png## 28/114: Finished tyrosine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00360._colored.png## 29/114: Finished phenylalanine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00380._colored.png## 30/114: Finished tryptophan_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00400._colored.png## 31/114: Finished phenylalanine,_tyrosine_and_tryptophan_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00410._colored.png## 32/114: Finished beta-alanine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00430._colored.png## 33/114: Finished taurine_and_hypotaurine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00450._colored.png## 34/114: Finished selenocompound_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00460._colored.png## 35/114: Finished cyanoamino_acid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00480._colored.png## 36/114: Finished glutathione_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00500._colored.png## 37/114: Finished starch_and_sucrose_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00510._colored.png## 38/114: Finished n-glycan_biosynthesis## Warning in data(bods): data set 'bods' not found## Warning: Number of mappable nodes is below 3, sce00511 skipped!## 39/114: Finished other_glycan_degradation## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00513._colored.png## 40/114: Finished various_types_of_n-glycan_biosynthesis## Warning in data(bods): data set 'bods' not found## Warning: Number of mappable nodes is below 3, sce00514 skipped!## 41/114: Finished other_types_of_o-glycan_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00520._colored.png## 42/114: Finished amino_sugar_and_nucleotide_sugar_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00561._colored.png## 43/114: Finished glycerolipid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00562._colored.png## 44/114: Finished inositol_phosphate_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00563._colored.png## 45/114: Finished glycosylphosphatidylinositol(gpi)-anchor_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00564._colored.png## 46/114: Finished glycerophospholipid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00565._colored.png## 47/114: Finished ether_lipid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00590._colored.png## 48/114: Finished arachidonic_acid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00592._colored.png## 49/114: Finished alpha-linolenic_acid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00600._colored.png## 50/114: Finished sphingolipid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00620._colored.png## 51/114: Finished pyruvate_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00630._colored.png## 52/114: Finished glyoxylate_and_dicarboxylate_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00640._colored.png## 53/114: Finished propanoate_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00650._colored.png## 54/114: Finished butanoate_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00660._colored.png## 55/114: Finished c5-branched_dibasic_acid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00670._colored.png## 56/114: Finished one_carbon_pool_by_folate## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00680._colored.png## 57/114: Finished methane_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00730._colored.png## 58/114: Finished thiamine_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00740._colored.png## 59/114: Finished riboflavin_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00750._colored.png## 60/114: Finished vitamin_b6_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00760._colored.png## 61/114: Finished nicotinate_and_nicotinamide_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00770._colored.png## 62/114: Finished pantothenate_and_coa_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00780._colored.png## 63/114: Finished biotin_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00785._colored.png## 64/114: Finished lipoic_acid_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00790._colored.png## 65/114: Finished folate_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00791._colored.png## 66/114: Finished atrazine_degradation## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00860._colored.png## 67/114: Finished porphyrin_and_chlorophyll_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00900._colored.png## Info: some node width is different from others, and hence adjusted!## 68/114: Finished terpenoid_backbone_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00909._colored.png## 69/114: Finished sesquiterpenoid_and_triterpenoid_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00910._colored.png## 70/114: Finished nitrogen_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00920._colored.png## 71/114: Finished sulfur_metabolism## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce00970._colored.png## 72/114: Finished aminoacyl-trna_biosynthesis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce01040._colored.png## 73/114: Finished biosynthesis_of_unsaturated_fatty_acids## Warning in data(bods): data set 'bods' not found## Warning: Parsing pathview_in/sce01100.xml file failed, please check the file!## 74/114: Finished metabolic_pathways## Warning in data(bods): data set 'bods' not found## Warning: Parsing pathview_in/sce01110.xml file failed, please check the file!## 75/114: Finished biosynthesis_of_secondary_metabolites## Warning in data(bods): data set 'bods' not found## Warning: Parsing pathview_in/sce01130.xml file failed, please check the file!## 76/114: Finished biosynthesis_of_antibiotics## Warning in data(bods): data set 'bods' not found## Warning: Parsing pathview_in/sce01200.xml file failed, please check the file!## 77/114: Finished carbon_metabolism## Warning in data(bods): data set 'bods' not found## Warning: Parsing pathview_in/sce01210.xml file failed, please check the file!## 78/114: Finished 2-oxocarboxylic_acid_metabolism## Warning in data(bods): data set 'bods' not found## Warning: Parsing pathview_in/sce01212.xml file failed, please check the file!## 79/114: Finished fatty_acid_metabolism## Warning in data(bods): data set 'bods' not found## Warning: Parsing pathview_in/sce01230.xml file failed, please check the file!## 80/114: Finished biosynthesis_of_amino_acids## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce02010._colored.png## 81/114: Finished abc_transporters## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03008._colored.png## 82/114: Finished ribosome_biogenesis_in_eukaryotes## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03010._colored.png## 83/114: Finished ribosome## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03013._colored.png## 84/114: Finished rna_transport## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03015._colored.png## 85/114: Finished mrna_surveillance_pathway## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03018._colored.png## 86/114: Finished rna_degradation## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03020._colored.png## 87/114: Finished rna_polymerase## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03022._colored.png## 88/114: Finished basal_transcription_factors## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03030._colored.png## 89/114: Finished dna_replication## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03040._colored.png## 90/114: Finished spliceosome## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03050._colored.png## 91/114: Finished proteasome## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03060._colored.png## 92/114: Finished protein_export## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03410._colored.png## 93/114: Finished base_excision_repair## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03420._colored.png## 94/114: Finished nucleotide_excision_repair## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03430._colored.png## 95/114: Finished mismatch_repair## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03440._colored.png## 96/114: Finished homologous_recombination## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce03450._colored.png## 97/114: Finished non-homologous_end-joining## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04011._colored.png## 98/114: Finished mapk_signaling_pathway_-_yeast## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04070._colored.png## 99/114: Finished phosphatidylinositol_signaling_system## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04111._colored.png## 100/114: Finished cell_cycle_-_yeast## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04113._colored.png## 101/114: Finished meiosis_-_yeast## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04120._colored.png## 102/114: Finished ubiquitin_mediated_proteolysis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04122._colored.png## 103/114: Finished sulfur_relay_system## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04130._colored.png## 104/114: Finished snare_interactions_in_vesicular_transport## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04139._colored.png## 105/114: Finished regulation_of_mitophagy_-_yeast## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04140._colored.png## 106/114: Finished regulation_of_autophagy## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04141._colored.png## 107/114: Finished protein_processing_in_endoplasmic_reticulum## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04144._colored.png## 108/114: Finished endocytosis## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04145._colored.png## 109/114: Finished phagosome## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04146._colored.png## 110/114: Finished peroxisome## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04213._colored.png## Info: some node width is different from others, and hence adjusted!## 111/114: Finished longevity_regulating_pathway_-_multiple_species## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04392._colored.png## 112/114: Finished hippo_signaling_pathway_-multiple_species## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04931._colored.png## 113/114: Finished insulin_resistance## Warning in data(bods): data set 'bods' not found## Info: Working in directory /cbcb/nelsayed-scratch/atb/rnaseq/scerevisiae_cbf5## Info: Writing image file sce04933._colored.png## 114/114: Finished age-rage_signaling_pathway_in_diabetic_complications