Organism : Bacillus cereus ATCC14579 | Module List :
BC4684

UDP-N-acetylmuramate--alanine ligase (NCBI ptt file)

CircVis
Functional Annotations (11)
Function System
UDP-N-acetylmuramate-alanine ligase cog/ cog
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of cell shape go/ biological_process
UDP-N-acetylmuramate-L-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
cell division go/ biological_process
D-Glutamine and D-glutamate metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
murC tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4684
(Mouseover regulator name to see its description)

BC4684 is regulated by 24 influences and regulates 0 modules.
Regulators for BC4684 (24)
Regulator Module Operator
BC0051 219 tf
BC1047 219 tf
BC1075 219 tf
BC1987 219 tf
BC2469 219 tf
BC4010 219 tf
BC4204 219 tf
BC4206 219 tf
BC4603 219 tf
BC5200 219 tf
BC5339 219 tf
BC5368 219 tf
BC0116 325 tf
BC0122 325 tf
BC0265 325 tf
BC0607 325 tf
BC2358 325 tf
BC3976 325 tf
BC4091 325 tf
BC4204 325 tf
BC4289 325 tf
BC4508 325 tf
BC4859 325 tf
BC5339 325 tf

Warning: BC4684 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
4354 9.90e+03 AGGCCG
Loader icon
4355 1.10e+04 GGATGcACC
Loader icon
4564 6.40e+00 ctttcacAAaTAcAtAAggGC
Loader icon
4565 4.50e+02 ggtAGaCTAgaaAatGTGaAa
Loader icon
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 BC4684

BC4684 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
UDP-N-acetylmuramate-alanine ligase cog/ cog
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
regulation of cell shape go/ biological_process
UDP-N-acetylmuramate-L-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
cell division go/ biological_process
D-Glutamine and D-glutamate metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
murC tigr/ tigrfam
Module neighborhood information for BC4684

BC4684 has total of 19 gene neighbors in modules 219, 325
Gene neighbors (19)
Gene Common Name Description Module membership
BC0051 BC0051 Pur operon repressor (NCBI ptt file) 219, 406
BC0257 BC0257 D-alanine--D-alanine ligase (NCBI ptt file) 169, 325
BC1075 BC1075 Beta-lactamase repressor (NCBI ptt file) 219, 440
BC1372 BC1372 D-alanine-activating enzyme (NCBI ptt file) 325, 513
BC1373 BC1373 hypothetical protein (NCBI ptt file) 325, 345
BC1416 BC1416 CDP-diacylglycerol--serine O-phosphatidyltransferase (NCBI ptt file) 64, 219
BC3924 BC3924 hypothetical Cytosolic Protein (NCBI ptt file) 219, 325
BC3929 BC3929 Phosphopantetheine adenylyltransferase (NCBI ptt file) 170, 219
BC4209 BC4209 Lipoate-protein ligase A (NCBI ptt file) 81, 325
BC4210 BC4210 Rhodanese-related sulfurtransferases (NCBI ptt file) 81, 325
BC4276 BC4276 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase (NCBI ptt file) 231, 325
BC4282 BC4282 Endonuclease IV (NCBI ptt file) 219, 325
BC4648 BC4648 Cysteine desulfhydrase (NCBI ptt file) 94, 325
BC4684 BC4684 UDP-N-acetylmuramate--alanine ligase (NCBI ptt file) 219, 325
BC4740 BC4740 TrkA C-terminal domain protein (NCBI ptt file) 219, 485
BC4746 BC4746 Fe-S oxidoreductase (NCBI ptt file) 325, 513
BC4747 BC4747 SAM-dependent methyltransferase (NCBI ptt file) 325, 513
BC5203 BC5203 Undecaprenyl-phosphate alpha-N-acetylglucosaminephosphotransferase (NCBI ptt file) 81, 325
BC5368 BC5368 Transcriptional regulator pfoR (NCBI ptt file) 219, 403
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 BC4684
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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