Organism : Bacillus subtilis | Module List :
BSU35620 lytC

N-acetylmuramoyl-L-alanine amidase (major autolysin) (RefSeq)

CircVis
Functional Annotations (3)
Function System
Putative cell wall-binding domain cog/ cog
N-acetylmuramoyl-L-alanine amidase activity go/ molecular_function
peptidoglycan catabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU35620
(Mouseover regulator name to see its description)

BSU35620 is regulated by 9 influences and regulates 0 modules.
Regulators for BSU35620 lytC (9)
Regulator Module Operator
BSU01430 2 tf
BSU16470 2 tf
BSU28410 2 tf
BSU09830 254 tf
BSU16470 254 tf
BSU25760 254 tf
BSU35430 254 tf
BSU35650 254 tf
BSU36420 254 tf

Warning: BSU35620 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 2 motifs predicted.

Motif Table (2)
Motif Id e-value Consensus Motif Logo
5448 7.10e-01 ATGgttATccTAAgaAatagCac
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5449 2.40e+01 TtGTTTTgcctTaCTtacaaaGtA
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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 BSU35620

BSU35620 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Putative cell wall-binding domain cog/ cog
N-acetylmuramoyl-L-alanine amidase activity go/ molecular_function
peptidoglycan catabolic process go/ biological_process
Module neighborhood information for BSU35620

BSU35620 has total of 38 gene neighbors in modules 2, 254
Gene neighbors (38)
Gene Common Name Description Module membership
BSU11140 yitU putative phosphatase (RefSeq) 70, 254
BSU11150 yitV putative hydrolase (RefSeq) 113, 254
BSU16180 flgB flagellar basal body rod protein FlgB (RefSeq) 254, 334
BSU16190 flgC flagellar basal body rod protein FlgC (RefSeq) 254, 334
BSU16200 fliE flagellar hook-basal body protein FliE (RefSeq) 254, 334
BSU16210 fliF flagellar MS-ring protein (RefSeq) 254, 334
BSU16220 fliG flagellar motor switch protein G (RefSeq) 254, 334
BSU16230 fliH flagellar assembly protein H (RefSeq) 254, 334
BSU16240 fliI flagellum-specific ATP synthase (RefSeq) 185, 254
BSU16250 fliJ flagellar biosynthesis chaperone (RefSeq) 185, 254
BSU16260 ylxF putative kinesin-like protein (RefSeq) 185, 254
BSU16270 fliK flagellar hook-length control protein (RefSeq) 185, 254
BSU16280 flgD flagellar basal body rod modification protein (RefSeq) 185, 254
BSU16290 flgG flagellar basal body rod protein FlgG (RefSeq) 185, 254
BSU16300 fliL flagellar basal body-associated protein FliL (RefSeq) 185, 254
BSU16310 fliM flagellar motor switch protein FliM (RefSeq) 185, 254
BSU16320 fliY flagellar motor switch protein (RefSeq) 185, 254
BSU16330 cheY regulator of chemotaxis and motility (RefSeq) 2, 254
BSU16340 fliZ flagella biosynthesis protein FliZ (RefSeq) 2, 382
BSU16350 fliP flagellar biosynthesis protein FliP (RefSeq) 2, 254
BSU16360 fliQ flagellar biosynthesis protein FliQ (RefSeq) 2, 45
BSU16370 fliR flagellar biosynthesis protein FliR (RefSeq) 2, 382
BSU16380 flhB flagellar biosynthesis protein FlhB (RefSeq) 2, 45
BSU16390 flhA flagellar biosynthesis protein FlhA (RefSeq) 2, 45
BSU16400 flhF flagellar biosynthesis regulator FlhF (RefSeq) 2, 45
BSU16410 ylxH essential component of the flagellar assembly machinery (RefSeq) 2, 45
BSU16420 cheB chemotaxis-specific methylesterase (RefSeq) 2, 45
BSU16430 cheA chemotactic two-component sensor histidine kinase (RefSeq) 2, 45
BSU16440 cheW modulation of CheA activity in response to attractants (chemotaxis) (RefSeq) 2, 45
BSU16450 cheC signal terminating phosphatase of CheR-mediated methylation of methyl-accepting chemotaxis proteins (MCPs) (RefSeq) 2, 235
BSU16460 cheD sequence specific deamidase required for methylation of methyl-accepting chemotaxis proteins (MCPs) by CheR (RefSeq) 2, 45
BSU16470 sigD RNA polymerase sigma factor SigD (RefSeq) 2, 382
BSU16480 ylxL coupling factor for flagellin transcription and translation (RefSeq) 2, 254
BSU23900 yqjF hypothetical protein (RefSeq) 254, 317
BSU35620 lytC N-acetylmuramoyl-L-alanine amidase (major autolysin) (RefSeq) 2, 254
BSU35630 lytB modifier protein of major autolysin LytC (RefSeq) 2, 254
VIMSS39609 VIMSS39609 None 2, 29
VIMSS39965 VIMSS39965 None 2, 235
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 BSU35620
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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