Analysis of networks of host proteins in the early time points following HIV transduction

Csősz, Éva; Tóth, Ferenc; Mahdi, Mohamed; Tsaprailis, George; Emri, Miklós; Tőzsér, József

doi:10.1186/s12859-019-2990-3

BMC Bioinformatics

Table 1 List of GO terms with significantly different changes in the functional sub-network in H04

From: Analysis of networks of host proteins in the early time points following HIV transduction

GO code	GO term	Significantly changed parameter	Direction of change in H04
GO.0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	Df	decrease
GO.0000228	nuclear chromosome	Df	decrease
GO.0000375	RNA splicing, via transesterification reactions	Df	decrease
GO.0000398	mRNA splicing, via spliceosome	Df	decrease
GO.0000956	nuclear-transcribed mRNA catabolic process	Df	decrease
GO.0003735	structural constituent of ribosome	Df	decrease
GO.0005198	structural molecule activity	Df	decrease
GO.0005515	protein binding	Df	decrease
GO.0005524	ATP binding	Df, Dc	decrease
GO.0005622	intracellular	Df	decrease
GO.0005737	cytoplasm	Df	decrease
GO.0005739	mitochondrion	Df	decrease
GO.0005840	ribosome	Df	decrease
GO.0006351	transcription, DNA-templated	Df, Dc	decrease
GO.0006366	transcription from RNA polymerase II promoter	Df, Dc	decrease
GO.0006367	transcription initiation from RNA polymerase II promoter	Df	decrease
GO.0006396	termination of RNA polymerase II transcription	Df	decrease
GO.0006397	mRNA processing	Df	decrease
GO.0006401	RNA catabolic process	Df	decrease
GO.0006402	mRNA catabolic process	Df	decrease
GO.0006412	translation	Df	decrease
GO.0006413	translational initiation	Df, Dc	decrease
GO.0006414	translational elongation	Df, Dc	decrease
GO.0006415	translational termination	Df	decrease
GO.0006417	regulation of translation	Df, Dc	decrease
GO.0006518	peptide metabolic process	Df	decrease
GO.0006605	protein targeting	Df	decrease
GO.0006614	SRP-dependent cotranslational protein targeting to membrane	Df	decrease
GO.0006732	coenzyme metabolic process	Df, Dc	decrease
GO.0006886	intracellular protein transport	Df	decrease
GO.0008104	protein localization	Rf	decrease
GO.0008152	metabolic process	Df	decrease
GO.0008380	RNA splicing	Df	decrease
GO.0009056	catabolic process	Df	decrease
GO.0009892	negative regulation of metabolic process	Df	decrease
GO.0009987	cellular process	Df	decrease
GO.0010468	regulation of gene expression	Df	decrease
GO.0010556	regulation of macromolecule biosynthetic process	Df	decrease
GO.0010608	posttranscriptional regulation of gene expression	Df, Dc	decrease
GO.0010941	regulation of cell death	Df	decrease
GO.0015031	protein transport	Df	decrease
GO.0016032	viral process	Df	increase
GO.0016043	cellular component organization	Df	decrease
GO.0016070	RNA metabolic process	Df, Dc	decrease
GO.0016071	mRNA metabolic process	Df	decrease
GO.0016482	cytoplasmic transport	Df	decrease
GO.0016604	nuclear body	Df, Dc	decrease
GO.0017076	purine nucleotide binding	Df, Dc	decrease
GO.0018130	heterocycle biosynthetic process	Df, Dc	decrease
GO.0019058	viral life cycle	Df	decrease
GO.0019080	viral gene expression	Df	decrease
GO.0019083	viral transcription	Df	decrease
GO.0019222	regulation of metabolic process	Df	decrease
GO.0019438	aromatic compound biosynthetic process	Df, Dc	decrease
GO.0019538	aromatic compound biosynthetic process	Df	decrease
GO.0019899	enzyme binding	Df	decrease
GO.0019900	kinase binding	Df, Dc	increase
GO.0019901	protein kinase binding	Df	increase
GO.0022607	cellular component assembly	Df	decrease
GO.0022626	cytosolic ribosome	Df	decrease
GO.0030554	adenyl nucleotide binding	Df, Dc	decrease
GO.0031625	ubiquitin protein ligase binding	Df, Dc	decrease
GO.0031974	membrane-enclosed lumen	Df	decrease
GO.0032550	purine ribonucleoside binding	Df, Dc	decrease
GO.0032553	ribonucleotide binding	Df, Dc	decrease
GO.0032555	purine ribonucleotide binding	Df, Dc	decrease
GO.0032774	RNA biosynthetic process	Df, Dc	decrease
GO.0034248	regulation of cellular amide metabolic process	Df	decrease
GO.0034613	cellular protein localization	Rf	decrease
GO.0034622	cellular macromolecular complex assembly	Df	decrease
GO.0034645	cellular macromolecule biosynthetic process	Df	decrease
GO.0034654	nucleobase-containing compound biosynthetic process	Df, Dc	decrease
GO.0034655	nucleobase-containing compound catabolic process	Df	decrease
GO.0035639	purine ribonucleoside triphosphate binding	Df, Dc	decrease
GO.0036094	small molecule binding	Df, Dc	decrease
GO.0042981	regulation of apoptotic process	Df	decrease
GO.0043065	positive regulation of apoptotic process	Df	decrease
GO.0043066	negative regulation of apoptotic process	Df, Dc	decrease
GO.0043226	organelle	Df	decrease
GO.0043227	membrane-bounded organelle	Df, Dc	decrease
GO.0043229	intracellular organelle	Df	decrease
GO.0043231	intracellular membrane-bounded organelle	Df	decrease
GO.0043233	organelle lumen	Df	decrease
GO.0044085	cellular component biogenesis	Df	decrease
GO.0044237	cellular metabolic process	Df	decrease
GO.0044238	primary metabolic process	Df	decrease
GO.0044248	cellular catabolic process	Df	decrease
GO.0044249	cellular biosynthetic process	Df	decrease
GO.0044260	cellular macromolecule metabolic process	Df	decrease
GO.0044265	cellular macromolecule catabolic process	Df	decrease
GO.0044267	cellular protein metabolic process	Df	decrease
GO.0044271	cellular nitrogen compound biosynthetic process	Df, Dc	decrease
GO.0044391	ribosomal subunit	Df	decrease
GO.0044422	organelle part	Df	decrease
GO.0044424	intracellular part	Df	decrease
GO.0044444	cytoplasmic part	Df	decrease
GO.0044446	intracellular organelle part	Df	decrease
GO.0044451	nucleoplasm part	Df, Dc	decrease
GO.0044454	nuclear chromosome part	Df	decrease
GO.0044802	single-organism membrane organization	Df, Dc	decrease
GO.0045184	establishment of protein localization	Df	decrease
GO.0046907	intracellular transport	Df, Dc	decrease
GO.0051084	de novo posttranslational protein folding	Df	increase
GO.0051704	multi-organism process	Df, Dc	increase
GO.0060255	regulation of macromolecule metabolic process	Df	decrease
GO.0060548	negative regulation of cell death	Df, Dc	decrease
GO.0065003	macromolecular complex assembly	Df	decrease
GO.0070013	intracellular organelle lumen	Df	decrease
GO.0070972	protein localization to endoplasmic reticulum	Rf	decrease
GO.0071013	catalytic step 2 spliceosome	Df	decrease
GO.0071702	organic substance transport	Df, Dc	decrease
GO.0071704	organic substance metabolic process	Df	decrease
GO.0071705	nitrogen compound transport	Df, Dc	decrease
GO.0071822	protein complex subunit organization	Df	increase
GO.0071840	cellular component organization or biogenesis	Df	decrease
GO.0072594	establishment of protein localization to organelle	Df	decrease
GO.0080090	regulation of primary metabolic process	Df	decrease
GO.0080135	regulation of cellular response to stress	Df, Dc	decrease
GO.0090304	nucleic acid metabolic process	Df, Dc	decrease
GO.0097367	carbohydrate derivative binding	Df, Dc	decrease
GO.1901362	organic cyclic compound biosynthetic process	Df, Dc	decrease
GO.1901566	organonitrogen compound biosynthetic process	Df	decrease
GO.1901575	organic substance catabolic process	Df	decrease
GO.1901576	organic substance biosynthetic process	Df	decrease
GO.1902580	single-organism cellular localization	Df	decrease

In case of each GO term where statistically significant changes were observed in network parameters in HIV-1 treated cells at 4 h time-point the GO identifier, the changed parameter and the direction of change is indicated

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ISSN: 1471-2105

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