Supplementary file: Interfacing cellular networks of S ... - BioMed Central
Supplementary file: Interfacing cellular networks of S. cerevisiae and E. coli: Connecting dynamic and genetic information Ricardo de Matos Simoes1 , Matthias Dehmer2 , Frank Emmert-Streib1∗ 1 Computational Biology and Machine Learning Laboratory Center for Cancer Research and Cell Biology School of Medicine, Dentistry and Biomedical Sciences Faculty of Medicine, Health and Life Sciences Queen’s University Belfast 97 Lisburn Road, Belfast, UK 2 Institute for Bioinformatics and Translational Research UMIT, Hall in Tyrol, Austria
∗
corresponding author: [email protected]
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Figure 1: Gene Ontology Biological Process enrichment analysis of the S. cerevisiae A) GRN-PPN interface (785 genes, 82 terms p f dr ≤ 0.01) and B) GRN-TRN interface (64 genes, 86 terms p f dr ≤ 0.01). 2
Figure 2: Gene Ontology Biological Process enrichment analysis of the S. cerevisiae TRN-PPN interface (115 genes, 96 terms p f dr ≤ 0.01).
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Figure 3: Gene Pair enrichment analysis of the S. cerevisiae GRN, PPN and TRN network. Shown are the shared significant Gene Ontology terms for A) GRN-PPN (top 150 terms from 249 pbon f ≤ 10e − 4) B) GRN-TRN 42 terms (pbon f ≤ 10e − 4) and C) TRN-PPN 75 terms (pbon f ≤ 10e − 4). In brackets after the term name shown the number of edges in the respective term for network 1 and network 2.
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Figure 4: Gene Pair enrichment analysis of the E. coli GRN, PPN and TRN network. Shown are the shared significant Gene Ontology terms for A) GRN-PPN (151 terms pbon f ≤ 10e − 4) B) GRN-TRN 63 terms (pbon f ≤ 10e − 4) and C) TRN-PPN 21 terms (pbon f ≤ 10e − 4). In brackets after the term name shown the number of edges in the respective term for network 1 and network 2. 5
GRN-PPN degree centrality spearman rank test for GO Biological Process (S. cerevisiae)
GO:0033674 positive regulation of kinase activity (74) r=0.41
GO:0010604 positive regulation of macromolecule metabolic process (931)
GO:0031401 positive regulation of protein modification process (758)
GO:0042724 thiamine−containing compound biosynthetic process (203) r=0.22
GO:0010382 cellular cell wall macromolecule metabolic process (129)
GO:0051170 nuclear import (697) r=0.15
GO:0006696 ergosterol biosynthetic process (203) r=0.22
GO:0031328 positive regulation of cellular biosynthetic process (766)
GO:0033692 cellular polysaccharide biosynthetic process (74) r=0.41 GO:0042775 GO:0009205 purine mitochondrial ribonucleoside ATP synthesis triphosphate coupled electron metabolic process transport (134) (697) r=0.15
GO:0046685 response to arsenic−containing substance (70) r=0.4
GO:0006289 GO:0006281 DNA GO:0006950 response nucleotide−excision repair (209) to stress repair (654) r=0.24 (70) r=0.4 r=0.14
GO:0019236 response to pheromone (745) r=0.13
GO:0006611 protein export from nucleus (217) r=0.24
GO:0005977 glycogen metabolic process (861) r=0.12 GO:0031938 GO:0010558 negative regulation regulation of of chromatin macromolecule silencing at biosynthetic telomere (246) process (785) GO:0010556 GO:0006348 chromatin regulation silencing at of macromolecule telomere (748) biosynthetic process r=0.13 (246) r=0.19
GO:0006338 chromatin remodeling (218) r=0.24
GO:0051052 regulation of DNA metabolic process (411) r=0.19
GO:0031145 anaphase−promoting complex−dependent proteasomal ubiquitin−dependent protein catabolic process (201) r=0.22
GO:0000070 mitotic sister chromatid segregation (928) r=0.11
GO:0051129 negative regulation of cellular component organization (638) GO:0001300 chronological cell aging (71) r=0.38
GO:0006623 protein targeting to vacuole (200) r=0.23
GO:0031990 mRNA export from nucleus in response to (786) r=0.12
GO:0000291 nuclear−transcribed mRNA catabolic process, exonucleolytic (203) r=0.22
GO:0000011 vacuole inheritance (764) r=0.12
Figure 5: GRN-PPN degree centrality Spearman’s rank test for GO Biological Process (S. cerevisiae). In brackets shown the number of genes shared between both networks of the corresponding GO term subnetworks and the centrality Spearman’s correlation coefficient ρ. Color gradient (red to yellow) denote the rank of the 32 shown terms with p f dr ≤ 0.05.
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∗
corresponding author: [email protected]
1
Figure 1: Gene Ontology Biological Process enrichment analysis of the S. cerevisiae A) GRN-PPN interface (785 genes, 82 terms p f dr ≤ 0.01) and B) GRN-TRN interface (64 genes, 86 terms p f dr ≤ 0.01). 2
Figure 2: Gene Ontology Biological Process enrichment analysis of the S. cerevisiae TRN-PPN interface (115 genes, 96 terms p f dr ≤ 0.01).
3
Figure 3: Gene Pair enrichment analysis of the S. cerevisiae GRN, PPN and TRN network. Shown are the shared significant Gene Ontology terms for A) GRN-PPN (top 150 terms from 249 pbon f ≤ 10e − 4) B) GRN-TRN 42 terms (pbon f ≤ 10e − 4) and C) TRN-PPN 75 terms (pbon f ≤ 10e − 4). In brackets after the term name shown the number of edges in the respective term for network 1 and network 2.
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Figure 4: Gene Pair enrichment analysis of the E. coli GRN, PPN and TRN network. Shown are the shared significant Gene Ontology terms for A) GRN-PPN (151 terms pbon f ≤ 10e − 4) B) GRN-TRN 63 terms (pbon f ≤ 10e − 4) and C) TRN-PPN 21 terms (pbon f ≤ 10e − 4). In brackets after the term name shown the number of edges in the respective term for network 1 and network 2. 5
GRN-PPN degree centrality spearman rank test for GO Biological Process (S. cerevisiae)
GO:0033674 positive regulation of kinase activity (74) r=0.41
GO:0010604 positive regulation of macromolecule metabolic process (931)
GO:0031401 positive regulation of protein modification process (758)
GO:0042724 thiamine−containing compound biosynthetic process (203) r=0.22
GO:0010382 cellular cell wall macromolecule metabolic process (129)
GO:0051170 nuclear import (697) r=0.15
GO:0006696 ergosterol biosynthetic process (203) r=0.22
GO:0031328 positive regulation of cellular biosynthetic process (766)
GO:0033692 cellular polysaccharide biosynthetic process (74) r=0.41 GO:0042775 GO:0009205 purine mitochondrial ribonucleoside ATP synthesis triphosphate coupled electron metabolic process transport (134) (697) r=0.15
GO:0046685 response to arsenic−containing substance (70) r=0.4
GO:0006289 GO:0006281 DNA GO:0006950 response nucleotide−excision repair (209) to stress repair (654) r=0.24 (70) r=0.4 r=0.14
GO:0019236 response to pheromone (745) r=0.13
GO:0006611 protein export from nucleus (217) r=0.24
GO:0005977 glycogen metabolic process (861) r=0.12 GO:0031938 GO:0010558 negative regulation regulation of of chromatin macromolecule silencing at biosynthetic telomere (246) process (785) GO:0010556 GO:0006348 chromatin regulation silencing at of macromolecule telomere (748) biosynthetic process r=0.13 (246) r=0.19
GO:0006338 chromatin remodeling (218) r=0.24
GO:0051052 regulation of DNA metabolic process (411) r=0.19
GO:0031145 anaphase−promoting complex−dependent proteasomal ubiquitin−dependent protein catabolic process (201) r=0.22
GO:0000070 mitotic sister chromatid segregation (928) r=0.11
GO:0051129 negative regulation of cellular component organization (638) GO:0001300 chronological cell aging (71) r=0.38
GO:0006623 protein targeting to vacuole (200) r=0.23
GO:0031990 mRNA export from nucleus in response to (786) r=0.12
GO:0000291 nuclear−transcribed mRNA catabolic process, exonucleolytic (203) r=0.22
GO:0000011 vacuole inheritance (764) r=0.12
Figure 5: GRN-PPN degree centrality Spearman’s rank test for GO Biological Process (S. cerevisiae). In brackets shown the number of genes shared between both networks of the corresponding GO term subnetworks and the centrality Spearman’s correlation coefficient ρ. Color gradient (red to yellow) denote the rank of the 32 shown terms with p f dr ≤ 0.05.
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