Organism : Bacillus subtilis | Module List :
BSU03010 amhX

amidohydrolase (RefSeq)

CircVis
Functional Annotations (5)
Function System
Metal-dependent amidase/aminoacylase/carboxypeptidase cog/ cog
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
protein dimerization activity go/ molecular_function
amidohydrolases tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU03010
(Mouseover regulator name to see its description)

BSU03010 is regulated by 30 influences and regulates 0 modules.
Regulators for BSU03010 amhX (30)
Regulator Module Operator
BSU04680 101 tf
BSU05640 101 tf
BSU08300 101 tf
BSU09990 101 tf
BSU10420 101 tf
BSU10860 101 tf
BSU20780 101 tf
BSU23450 101 tf
BSU29630 101 tf
BSU34170 101 tf
BSU35490 101 tf
BSU36020 101 tf
BSU37080 101 tf
BSU38600 101 tf
BSU05050 136 tf
BSU05640 136 tf
BSU07590 136 tf
BSU09330 136 tf
BSU09510 136 tf
BSU09650 136 tf
BSU09990 136 tf
BSU10150 136 tf
BSU10860 136 tf
BSU15330 136 tf
BSU19030 136 tf
BSU23450 136 tf
BSU28550 136 tf
BSU29690 136 tf
BSU29740 136 tf
BSU33740 136 tf

Warning: BSU03010 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
5156 4.00e-05 aaAAAGaggGg
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5157 1.90e+02 gCcTtcCtcttgttA
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5224 5.90e-01 AaAAAggagagGcgt
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5225 1.00e+03 gcgGaAaGgcgtT
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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 BSU03010

BSU03010 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Metal-dependent amidase/aminoacylase/carboxypeptidase cog/ cog
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
protein dimerization activity go/ molecular_function
amidohydrolases tigr/ tigrfam
Module neighborhood information for BSU03010

BSU03010 has total of 42 gene neighbors in modules 101, 136
Gene neighbors (42)
Gene Common Name Description Module membership
BSU02820 rapJ response regulator aspartate phosphatase (RefSeq) 101, 215
BSU03010 amhX amidohydrolase (RefSeq) 101, 136
BSU04130 yczJ hypothetical protein (RefSeq) 101, 310
BSU04210 ydaF putative ribosomal protein N-acetyltransferase (RefSeq) 68, 101
BSU09670 dat D-alanine aminotransferase (RefSeq) 101, 136
BSU09990 hpr transcriptional regulator Hpr (RefSeq) 101, 393
BSU10070 yhaA putative amidohydrolase (RefSeq) 101, 381
BSU10200 yhfE putative endoglucanase (RefSeq) 101, 296
BSU10210 yhfF hypothetical protein (RefSeq) 90, 101
BSU10860 yisT hypothetical protein (RefSeq) 101, 171
BSU11840 yjcF putative acetyltransferase (RefSeq) 101, 296
BSU11850 yjcG hypothetical protein (RefSeq) 101, 296
BSU11860 yjcH putative hydrolase (RefSeq) 101, 296
BSU12210 yjiB putative monooxygenase (cytochrome P450) (RefSeq) 101, 114
BSU12220 yjiC putative glycosyltransferase (RefSeq) 101, 114
BSU12920 dppA D-alanyl-aminopeptidase (RefSeq) 134, 136
BSU12930 dppB dipeptide ABC transporter (permease) (RefSeq) 134, 136
BSU12940 dppC dipeptide ABC transporter (permease) (RefSeq) 134, 136
BSU12950 dppD dipeptide ABC transporter (ATP-binding protein) (RefSeq) 134, 136
BSU12960 dppE dipeptide ABC transporter (dipeptide-binding lipoprotein) (RefSeq) 134, 136
BSU12970 ykfA putative L,D-carboxypeptidase (RefSeq) 134, 136
BSU12980 ykfB L-Ala-D/L-Glu epimerase (RefSeq) 134, 136
BSU12990 ykfC cell wall endopeptidase (RefSeq) 134, 136
BSU13000 ykfD putative cell wall oligopeptide ABC transporter (ATP binding protein) (RefSeq) 134, 136
BSU18350 dacC D-alanyl-D-alanine carboxypeptidase (RefSeq) 136, 287
BSU18360 yoxA putative epimerase (RefSeq) 136, 287
BSU31330 yugN hypothetical protein (RefSeq) 134, 136
BSU31340 yugM putative transporter (RefSeq) 134, 136
BSU32080 yuiB hypothetical protein (RefSeq) 101, 171
BSU32090 yuiA hypothetical protein (RefSeq) 101, 171
BSU35980 ywsA hypothetical protein (RefSeq) 134, 136
BSU36520 glnK nitrogen-regulated PII-like regulator protein (RefSeq) 68, 101
BSU36640 ureC urease subunit alpha (RefSeq) 101, 136
BSU36650 ureB urease (beta subunit) (RefSeq) 101, 136
BSU36660 ureA urease subunit gamma (RefSeq) 101, 136
BSU38090 vpr extracellular serine protease (RefSeq) 19, 101
BSU38470 ywaD double-zinc aminopeptidase (RefSeq) 101, 287
BSU39330 abnB arabinan endo-1,5-alpha-L-arabinosidase (RefSeq) 136, 323
BSU40250 yycR putative dehydrogenase (RefSeq) 136, 287
BSU40300 rapG response regulator aspartate phosphatase (RefSeq) 101, 287
BSU40310 phrG secreted regulator of the activity of phosphatase RapG (RefSeq) 101, 171
VIMSS37491 VIMSS37491 None 101, 136
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 BSU03010
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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