Organism : Rhodobacter sphaeroides 2.4.1 | Module List :
RSP_2100 murF

UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase (NCBI)

CircVis
Functional Annotations (12)
Function System
UDP-N-acetylmuramyl pentapeptide synthase cog/ cog
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of cell shape go/ biological_process
UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity go/ molecular_function
cell division go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
murF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for RSP_2100
(Mouseover regulator name to see its description)

RSP_2100 is regulated by 31 influences and regulates 0 modules.
Regulators for RSP_2100 murF (31)
Regulator Module Operator
RSP_0386 374 tf
RSP_0395 374 tf
RSP_0415 374 tf
RSP_0623 374 tf
RSP_1014 374 tf
RSP_1225 374 tf
RSP_1435 374 tf
RSP_1890 374 tf
RSP_2026 374 tf
RSP_2171 374 tf
RSP_2346 374 tf
RSP_2533 374 tf
RSP_2801 374 tf
RSP_2838 374 tf
RSP_2840 374 tf
RSP_2965 374 tf
RSP_3665 374 tf
RSP_0415 383 tf
RSP_0623 383 tf
RSP_0698 383 tf
RSP_1225 383 tf
RSP_1712 383 tf
RSP_1776 383 tf
RSP_2026 383 tf
RSP_2425 383 tf
RSP_2533 383 tf
RSP_2801 383 tf
RSP_2838 383 tf
RSP_2850 383 tf
RSP_2950 383 tf
RSP_3298 383 tf

Warning: RSP_2100 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
8440 6.40e+02 AacGgAAgaGg
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8441 1.80e+04 AAAGTT
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8456 2.20e+01 agGcgcCctTctTtttgG
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8457 2.00e+03 ttCttGgaAA
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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_2100

RSP_2100 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
UDP-N-acetylmuramyl pentapeptide synthase cog/ cog
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of cell shape go/ biological_process
UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity go/ molecular_function
cell division go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
murF tigr/ tigrfam
Module neighborhood information for RSP_2100

RSP_2100 has total of 46 gene neighbors in modules 374, 383
Gene neighbors (46)
Gene Common Name Description Module membership
RSP_0313 RSP_0313 hypothetical protein (NCBI) 115, 383
RSP_0652 RSP_0652 UDP-glucose 4-epimerase (NCBI) 130, 374
RSP_0653 RSP_0653 UDP-glucose 6-dehydrogenase (NCBI) 33, 374
RSP_0702 RSP_0702 ABC peptide transporter, inner membrane subunit (NCBI) 130, 374
RSP_0703 RSP_0703 ABC peptide transporter, inner membrane subunit (NCBI) 130, 374
RSP_0721 PmtA Phosphatidylethanolamine N-methyltransferase (NCBI) 339, 374
RSP_0781 RSP_0781 polyphosphate kinase (NCBI) 130, 374
RSP_0818 carB carbamoyl phosphate synthase large subunit (RefSeq) 209, 383
RSP_1108 TruB tRNA pseudouridine synthase B (NCBI) 209, 383
RSP_1166 mutT NTP pyrophosphohydrolase (NCBI) 259, 374
RSP_1288 RSP_1288 ABC branched chain amino acid family transporter, ATPase subunit (NCBI) 263, 383
RSP_1290 RSP_1290 ABC branched chain amino acid family transporter, inner membrane subunit (NCBI) 263, 383
RSP_1568 RSP_1568 Glutamine synthetase (NCBI) 114, 374
RSP_1569 RSP_1569 probable aminotransferase (NCBI) 130, 374
RSP_1570 purK Phosphoribosylaminoimidazole carboxylase, ATPase subunit (NCBI) 7, 374
RSP_1670 spoT/relA RelA/SpoT family protein (NCBI) 130, 383
RSP_1675 rnc Ribonuclease III (NCBI) 263, 383
RSP_1677 RSP_1677 hypothetical protein (NCBI) 221, 383
RSP_1712 rpoC RNA polymerase I subunit A, (NCBI) 104, 383
RSP_1810 mviN putative virulence factor, MviN (NCBI) 221, 374
RSP_1811 glnD uridylyltransferase (NCBI) 221, 374
RSP_1950 RSP_1950 hypothetical protein (NCBI) 213, 383
RSP_2097 RSP_2097 Putative FtsL (NCBI) 374, 383
RSP_2098 ftsI Cell division protein FtsI/penicillin-binding protein 2 (NCBI) 326, 374
RSP_2099 murE UDP-N-acetylmuramoylalanyl-D-glutamate-2, 6-diaminopimelate ligase (NCBI) 374, 383
RSP_2100 murF UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate--D-alanyl-D-alanine ligase (NCBI) 374, 383
RSP_2101 mraY Phospho-N-acetylmuramoyl-pentapeptidetransferase (NCBI) 374, 383
RSP_2170 RSP_2170 Phosphate transporter, Pit family (NCBI) 263, 383
RSP_2256 dtd D-tyrosyl-tRNA(Tyr) deacylase (NCBI) 221, 374
RSP_2257 RSP_2257 putative Fructokinase (NCBI) 221, 374
RSP_2327 RSP_2327 hypothetical protein (NCBI) 356, 383
RSP_2403 RSP_2403 ABC cobalamin/Fe3+-siderophore transporter, periplasmic substrate-binding subunit (NCBI) 167, 383
RSP_2404 RSP_2404 ABC cobalamin/Fe3+-siderophore transporter, inner membrane subunit (NCBI) 167, 383
RSP_2405 RSP_2405 ABC cobalamin/Fe3+-siderophore transporter, ATPase subunit (NCBI) 167, 383
RSP_2406 RSP_2406 hypothetical protein (NCBI) 167, 383
RSP_2459 RSP_2459 ABC transporter, inner membrane subunit (NCBI) 87, 374
RSP_2612 fabH 3-oxoacyl-(acyl-carrier-protein) synthase III (NCBI) 263, 383
RSP_2613 plsX Fatty acid/phospholipid biosynthesis enzyme (NCBI) 263, 374
RSP_2648 RSP_2648 hypothetical protein (NCBI) 209, 383
RSP_2707 uppS Undecaprenyl pyrophosphate synthase (NCBI) 130, 374
RSP_2708 cdsA Phosphatidate cytidylyltransferase (NCBI) 130, 374
RSP_2917 RSP_2917 putative cystathionine gamma-synthase beta-lyase (NCBI) 7, 383
RSP_3712 RSP_3712 Multisubunit Na+/H+ antiporter MnhE subunit (NCBI) 311, 383
RSP_3713 RSP_3713 pH adaptation potassium efflux system, phaD subunit (NCBI) 311, 383
RSP_3719 RSP_3719 Polysaccharide export transporter, PST Family (NCBI) 5, 374
RSP_3720 RSP_3720 hypothetical protein (NCBI) 5, 374
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_2100
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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