Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2894 ndk

Nucleoside diphosphate kinase (NCBI)

CircVis
Functional Annotations (10)
Function System
Nucleoside diphosphate kinase cog/ cog
nucleoside diphosphate kinase activity go/ molecular_function
ATP binding go/ molecular_function
GTP biosynthetic process go/ biological_process
UTP biosynthetic process go/ biological_process
CTP biosynthetic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2894
(Mouseover regulator name to see its description)

RSP_2894 is regulated by 24 influences and regulates 0 modules.
Regulators for RSP_2894 ndk (24)
Regulator Module Operator
RSP_0087 345 tf
RSP_0327 345 tf
RSP_0394 345 tf
RSP_0591 345 tf
RSP_0611 345 tf
RSP_0698 345 tf
RSP_1139 345 tf
RSP_1669 345 tf
RSP_1776 345 tf
RSP_2425 345 tf
RSP_2853 345 tf
RSP_3022 345 tf
RSP_0327 15 tf
RSP_0755 15 tf
RSP_1231 15 tf
RSP_1739 15 tf
RSP_2236 15 tf
RSP_2533 15 tf
RSP_2681 15 tf
RSP_2838 15 tf
RSP_2840 15 tf
RSP_2922 15 tf
RSP_2950 15 tf
RSP_3095 15 tf

Warning: RSP_2894 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
7750 2.50e-05 atCGggAcagAAGG
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7751 1.60e-02 tGAAGGCtCTcCtCGGaaGcaTG
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8392 5.00e-05 ACaaAaGgTCc.GCct.tGaTc.A
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8393 1.60e-01 aaaatGcTGagtcaGAataGcACa
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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_2894

RSP_2894 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Nucleoside diphosphate kinase cog/ cog
nucleoside diphosphate kinase activity go/ molecular_function
ATP binding go/ molecular_function
GTP biosynthetic process go/ biological_process
UTP biosynthetic process go/ biological_process
CTP biosynthetic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for RSP_2894

RSP_2894 has total of 36 gene neighbors in modules 15, 345
Gene neighbors (36)
Gene Common Name Description Module membership
RSP_0165 RSP_0165 hypothetical protein (NCBI) 58, 345
RSP_0197 clpP Protease subunit of ATP-dependent Clp proteases (NCBI) 48, 345
RSP_0239 PntB Pyridine nucleotide transhydrogenase beta subunit (NCBI) 15, 203
RSP_0240 pntA Pyridine nucleotide transhydrogenase alpha subunit (NCBI) 15, 203
RSP_0479 RSP_0479 Elongation factor P (EF-P) (NCBI) 345, 369
RSP_0568 RSP_0568 Isoleucyl-tRNA synthetase, class Ia (NCBI) 15, 258
RSP_0865 RSP_0865 hypothetical protein (NCBI) 107, 345
RSP_1035 atpF FoF1 ATP synthase, subunit B (NCBI) 15, 369
RSP_1036 atpX FoF1 ATP synthase, subunit B (NCBI) 15, 369
RSP_1037 atpE FoF1 ATP synthase, subunit C (NCBI) 15, 369
RSP_1038 atpB FoF1 ATP synthase, subunit A (NCBI) 15, 369
RSP_1388 RSP_1388 DNA-binding protein HU, form N (NCBI) 327, 345
RSP_1529 trxA Thioredoxin (NCBI) 327, 345
RSP_1593 RSP_1593 NAD dependent malic enzyme (NCBI) 15, 25
RSP_1594 cdd Cytidine deaminase (NCBI) 15, 207
RSP_1595 RSP_1595 Thymidine phosphorylase (NCBI) 15, 25
RSP_1596 deoB probable phosphopentomutase protein (NCBI) 15, 174
RSP_1597 add adenosine deaminase (NCBI) 15, 174
RSP_1598 RSP_1598 putative uracil phosphoribosyltransferase (NCBI) 15, 25
RSP_1875 RSP_1875 hypothetical protein (NCBI) 345, 372
RSP_1937 InfC Translation initiation factor IF-3 (NCBI) 317, 345
RSP_1995 gltX Glutamyl-tRNA synthetase (NCBI) 15, 258
RSP_2298 atpG ATP synthase, gamma subunit (NCBI) 15, 369
RSP_2299 atpD F1-ATP synthase beta subunit (NCBI) 15, 369
RSP_2300 atpC ATP synthase, delta/epsilon subunit (NCBI) 15, 369
RSP_2463 acpP Acyl carrier protein (ACP) (NCBI) 327, 345
RSP_2615 RSP_2615 hypothetical protein (NCBI) 109, 345
RSP_2653 RSP_2653 ATPase, AAA family (NCBI) 223, 345
RSP_2654 RSP_2654 DnaK suppressor protein, DksA family (NCBI) 223, 345
RSP_2737 RSP_2737 Putative ssRNA endoribonuclease L-PSP (NCBI) 166, 345
RSP_2894 ndk Nucleoside diphosphate kinase (NCBI) 15, 345
RSP_2895 RSP_2895 putative ABC transporter, fused ATPase subunits (NCBI) 15, 160
RSP_2896 RSP_2896 Multiple antibiotic transporter (NCBI) 15, 234
RSP_3074 ilvD Dihydroxy-acid and 6-phosphogluconate dehydratase (NCBI) 15, 309
RSP_4041 tyrS Tyrosyl-tRNA synthetase, class Ib (NCBI) 15, 258
RSP_4042 RSP_4042 Peptidyl-prolyl cis-trans isomerase, cyclophilin type (NCBI) 166, 345
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_2894
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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