Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0823 SHMT

serine hydroxymethyltransferase protein (NCBI)

CircVis
Functional Annotations (12)
Function System
Glycine/serine hydroxymethyltransferase cog/ cog
glycine hydroxymethyltransferase activity go/ molecular_function
glycine metabolic process go/ biological_process
L-serine metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Cyanoamino acid metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0823
(Mouseover regulator name to see its description)

RSP_0823 is regulated by 22 influences and regulates 0 modules.
Regulators for RSP_0823 SHMT (22)
Regulator Module Operator
RSP_0402 71 tf
RSP_0728 71 tf
RSP_0958 71 tf
RSP_1077 71 tf
RSP_1163 71 tf
RSP_1231 71 tf
RSP_1272 71 tf
RSP_1274 71 tf
RSP_1890 71 tf
RSP_1925 71 tf
RSP_2130 71 tf
RSP_2236 71 tf
RSP_2610 71 tf
RSP_2801 71 tf
RSP_2922 71 tf
RSP_3238 71 tf
RSP_3528 71 tf
RSP_1231 85 tf
RSP_2606 85 tf
RSP_2888 85 tf
RSP_2963 85 tf
RSP_3238 85 tf

Warning: RSP_0823 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
7862 1.80e+00 aAGGGctaagtCaAtTTgGAgcAt
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7863 4.80e+03 CctTtgCCaGa
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7890 5.80e+00 gAaactTCCaa
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7891 4.80e+02 AAAAGgGcgct
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for RSP_0823

RSP_0823 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
Glycine/serine hydroxymethyltransferase cog/ cog
glycine hydroxymethyltransferase activity go/ molecular_function
glycine metabolic process go/ biological_process
L-serine metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Glycine serine and threonine metabolism kegg/ kegg pathway
Cyanoamino acid metabolism kegg/ kegg pathway
One carbon pool by folate kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for RSP_0823

RSP_0823 has total of 41 gene neighbors in modules 71, 85
Gene neighbors (41)
Gene Common Name Description Module membership
RSP_0549 RSP_0549 hypothetical protein (NCBI) 71, 171
RSP_0590 RSP_0590 hypothetical protein (NCBI) 85, 382
RSP_0769 RSP_0769 Glutathione S-transferase (NCBI) 23, 71
RSP_0823 SHMT serine hydroxymethyltransferase protein (NCBI) 71, 85
RSP_0880 dadA putative oxidoreductase, possibly D-amino acid oxidase protein (NCBI) 85, 100
RSP_0885 SseA Thiosulfate sulfurtransferase, Rhodanese-like (NCBI) 71, 171
RSP_0924 cinA Predicted nucleotide-utilizing enzyme/competence-damage associated protein (NCBI) 71, 286
RSP_1008 RSP_1008 4-hydroxybenzoate octaprenyltransferase (NCBI) 71, 164
RSP_1009 RSP_1009 possible outer membrane protein, OmpA family (NCBI) 71, 164
RSP_1033 RSP_1033 OmpA family protein (NCBI) 16, 71
RSP_1175 ubiG 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4 benzoquinol methylase (NCBI) 85, 108
RSP_1338 ubiE methyltransferase (NCBI) 85, 108
RSP_1351 serC phosphoserine aminotransferase (NCBI) 85, 360
RSP_1352 RSP_1352 D-3-phosphoglycerate dehydrogenase (NCBI) 85, 360
RSP_1460 RSP_1460 hypothetical protein (NCBI) 71, 93
RSP_1489 RSP_1489 Protein containing thioredoxin domain (NCBI) 30, 71
RSP_1513 trpB Putative Tryptophan synthase beta chain (NCBI) 85, 382
RSP_1665 RSP_1665 putative RhtB family transporter (NCBI) 81, 85
RSP_1666 LytB 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (NCBI) 81, 85
RSP_1760 RSP_1760 hypothetical protein (NCBI) 71, 377
RSP_1808 trpS tryptophanyl-tRNA synthetase (NCBI) 71, 360
RSP_1843 ftsY Signal recognition particle-docking protein FtsY (NCBI) 71, 309
RSP_1851 metZ O-succinylhomoserine sulfhydrylase (NCBI) 71, 360
RSP_2007 RSP_2007 conservd hypothetical protein (NCBI) 64, 71
RSP_2147 cysK O-acetylserine (Thiol)-lyase, cysteine synthase (NCBI) 71, 184
RSP_2193 gcvT predicted aminomethyltransferase, tetrahydrofolate dependent (NCBI) 71, 309
RSP_2313 RSP_2313 D-isomer specific 2-hydroxyacid dehydrogenase (NCBI) 85, 118
RSP_2336 RSP_2336 hypothetical protein (NCBI) 71, 181
RSP_2387 RSP_2387 hypothetical protein (NCBI) 71, 286
RSP_2408 RSP_2408 hypothetical protein (NCBI) 71, 322
RSP_2453 RSP_2453 putative oxidoreductase (NAD/NADP dependent) (NCBI) 71, 166
RSP_2768 RSP_2768 5-methyltetrahydrofolate S-homocysteine methyltransferase (NCBI) 27, 71
RSP_2835 ispD Probable 4-diphosphocytidyl-2C-methyl-D-erythritol synthase (YgbP) (NCBI) 85, 100
RSP_2848 hemB Delta-aminolevulinic acid dehydratase (Porphobilinogen synthase) (NCBI) 85, 382
RSP_2963 RSP_2963 transcriptional regulator, Crp-Fnr family (NCBI) 85, 139
RSP_2975 RSP_2975 hypothetical protein (NCBI) 71, 309
RSP_2985 RSP_2985 hypothetical protein (NCBI) 71, 181
RSP_2986 RSP_2986 ArgE/DapE/Acy1 family protein (NCBI) 52, 71
RSP_2987 RSP_2987 probable acetyltransferase (NCBI) 71, 181
RSP_3341 RSP_3341 Protein of unknown function UPF0074 (NCBI) 85, 172
RSP_3595 metK S-adenosylmethionine synthetase (NCBI) 43, 85
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for RSP_0823
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend