Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_0578

Adenylate kinase (NCBI)

CircVis
Functional Annotations (8)
Function System
Adenylate kinase and related kinases cog/ cog
adenylate kinase activity go/ molecular_function
ATP binding go/ molecular_function
nucleobase-containing compound metabolic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
adk tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_0578
(Mouseover regulator name to see its description)

RSP_0578 is regulated by 31 influences and regulates 0 modules.
Regulators for RSP_0578 (31)
Regulator Module Operator
RSP_0032 86 tf
RSP_0457 86 tf
RSP_1055 86 tf
RSP_1220 86 tf
RSP_1225 86 tf
RSP_1660 86 tf
RSP_1739 86 tf
RSP_1945 86 tf
RSP_2130 86 tf
RSP_2591 86 tf
RSP_2838 86 tf
RSP_2882 86 tf
RSP_3042 86 tf
RSP_3094 86 tf
RSP_3165 86 tf
RSP_3620 86 tf
RSP_0122 117 tf
RSP_0415 117 tf
RSP_1092 117 tf
RSP_1163 117 tf
RSP_1220 117 tf
RSP_1272 117 tf
RSP_1890 117 tf
RSP_2026 117 tf
RSP_2236 117 tf
RSP_2346 117 tf
RSP_2425 117 tf
RSP_2533 117 tf
RSP_2950 117 tf
RSP_3324 117 tf
RSP_3464 117 tf

Warning: RSP_0578 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
7892 5.50e-11 T.aaaataAagaaGatCGaTccgt
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7893 8.30e-05 ATaaG.cA.tcaaGG.gGAAA
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7954 7.30e-09 aaAccacGtcacAAaTgaGTgAT
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7955 2.00e-03 aCccaTatagaAagtGgCaaAAaA
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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_0578

RSP_0578 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Adenylate kinase and related kinases cog/ cog
adenylate kinase activity go/ molecular_function
ATP binding go/ molecular_function
nucleobase-containing compound metabolic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
adk tigr/ tigrfam
Module neighborhood information for RSP_0578

RSP_0578 has total of 29 gene neighbors in modules 86, 117
Gene neighbors (29)
Gene Common Name Description Module membership
RSP_0122 cerR transcriptional regulator, LuxR family (NCBI) 117, 298
RSP_0576 RSP_0576 Na+/solute symporter (NCBI) 86, 291
RSP_0577 RSP_0577 hypothetical protein (NCBI) 86, 291
RSP_0578 RSP_0578 Adenylate kinase (NCBI) 86, 117
RSP_0579 RSP_0579 Acetyl-coenzyme A synthetase (NCBI) 86, 117
RSP_1176 xylA Xylose isomerase (NCBI) 86, 363
RSP_1177 xylB Xylulose kinase (NCBI) 86, 363
RSP_1178 RSP_1178 ABC sugar (xylose) transporter, ATPase subunit (NCBI) 86, 363
RSP_1179 xylH ABC sugar (xylose) transporter, inner membrane subunit (NCBI) 86, 363
RSP_1180 xylF ABC sugar (xylose) transporter, periplasmic binding protein (NCBI) 86, 363
RSP_1181 xylR xylose operon repressor (NCBI) 86, 363
RSP_1939 RSP_1939 NADPH-ferredoxin reductase (NCBI) 86, 185
RSP_1940 RSP_1940 hypothetical protein (NCBI) 5, 86
RSP_1941 cysH Phosphoadenosine phosphosulfate reductase (NCBI) 5, 86
RSP_1942 RSP_1942 Sulfite/nitrite reductase hemoprotein subunit (NCBI) 5, 86
RSP_1943 RSP_1943 hypothetical protein (NCBI) 86, 180
RSP_1944 RSP_1944 Uroporphiryn-III C-methyltransferase/siroheme synthase (NCBI) 86, 180
RSP_1945 RSP_1945 Transcriptional Regulator, AsnC family (NCBI) 86, 185
RSP_2092 RSP_2092 Putative uvrD/DNA Helicase II (NCBI) 117, 237
RSP_2224 RSP_2224 multidrug efflux pump, membrane fusion protein (MFP) family (NCBI) 117, 171
RSP_2225 RSP_2225 hypothetical protein (NCBI) 117, 280
RSP_2658 RSP_2658 HesB/YadR/YfhF family protein (NCBI) 3, 117
RSP_2659 dgt Deoxyguanosinetriphosphate triphosphohydrolase (NCBI) 117, 316
RSP_2660 RSP_2660 Ribonuclease BN family protein (NCBI) 117, 242
RSP_3305 abc1 putative ubiquinol-cytochrome-c reductase assembly protein (NCBI) 117, 280
RSP_3696 cysA ABC sulfate/thiosulfate transporter, ATPase subunit CysA (NCBI) 32, 86
RSP_3697 cysP ABC sulfate/thiosulfate transporter, periplasmic binding protein CysP (NCBI) 32, 86
RSP_3698 cysT ABC sulfate/thiosulfate transporter, inner membrane subunit CysT (NCBI) 32, 86
RSP_3699 cysW ABC sulfate/thiosulfate transporter, inner membrane subunit CysW (NCBI) 32, 86
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_0578
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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