Organism : Bacillus subtilis | Module List :
BSU18850 yobD

transcriptional regulator (phage-related, Xre family) (RefSeq)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU18850
(Mouseover regulator name to see its description)

BSU18850 is regulated by 30 influences and regulates 4 modules.
Regulators for BSU18850 yobD (30)
Regulator Module Operator
BSU05330 202 tf
BSU08300 202 tf
BSU09560 202 tf
BSU10860 202 tf
BSU18850 202 tf
BSU23210 202 tf
BSU29740 202 tf
BSU33740 202 tf
BSU33970 202 tf
BSU35200 202 tf
BSU37080 202 tf
BSU39990 202 tf
BSU00230 155 tf
BSU11500 155 tf
BSU15330 155 tf
BSU15690 155 tf
BSU18850 155 tf
BSU19050 155 tf
BSU23090 155 tf
BSU23100 155 tf
BSU23520 155 tf
BSU25760 155 tf
BSU28820 155 tf
BSU29740 155 tf
BSU30020 155 tf
BSU33840 155 tf
BSU33970 155 tf
BSU35650 155 tf
BSU36160 155 tf
BSU37580 155 tf

Warning: BSU18850 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
5258 6.50e+01 cggCagTTtCC
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5259 2.10e+03 GGagGA.atag
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5348 3.70e+00 cggaatttTtTTT.T
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5349 1.00e+04 GGAGGgAT
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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 BSU18850

BSU18850 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BSU18850

BSU18850 has total of 37 gene neighbors in modules 155, 202
Gene neighbors (37)
Gene Common Name Description Module membership
BSU02260 ybfK carboxylesterase NP (RefSeq) 11, 155
BSU02800 ycdC putative hydrolase (RefSeq) 11, 202
BSU04010 sipU type I signal peptidase (RefSeq) 155, 313
BSU09570 yhdR aspartate aminotransferase (RefSeq) 155, 247
BSU11170 yitY putative FMN/FAD-binding oxidoreductase (RefSeq) 155, 313
BSU11620 yjbO pseudouridylate synthase (RefSeq) 155, 187
BSU12480 yjqB putative PBSX phage-related replication protein (RefSeq) 89, 202
BSU12860 ykbA putative amino acid permease (RefSeq) 202, 322
BSU14500 ykqA hypothetical protein (RefSeq) 155, 247
BSU15440 ylyA hypothetical protein (RefSeq) 202, 300
BSU15830 yloU hypothetical protein (RefSeq) 63, 155
BSU16750 asd aspartate-semialdehyde dehydrogenase (RefSeq) 155, 334
BSU16780 rnjB ribonuclease J2 (RefSeq) 155, 289
BSU16790 tepA protein export-enhancing factor (RefSeq) 177, 202
BSU18470 proJ gamma-glutamyl kinase (RefSeq) 202, 344
BSU18480 proH pyrroline-5-carboxylate reductase (RefSeq) 202, 344
BSU18850 yobD transcriptional regulator (phage-related, Xre family) (RefSeq) 155, 202
BSU19250 yocL hypothetical protein (RefSeq) 202, 411
BSU21770 ilvA threonine dehydratase (RefSeq) 102, 155
BSU24880 yqgO hypothetical protein (RefSeq) 89, 202
BSU25170 yqfO hypothetical protein (RefSeq) 202, 293
BSU25180 trmK tRNA: m1A22 methyltransferase (RefSeq) 1, 202
BSU27640 yrvC putative potassium transport accessory component (RefSeq) 170, 202
BSU27650 secDF bifunctional preprotein translocase subunit SecD/SecF (RefSeq) 155, 273
BSU28370 rph ribonuclease PH (RefSeq) 155, 187
BSU28840 ysdA putative membrane component (RefSeq) 72, 202
BSU29150 ytwI putative integral inner membrane protein (RefSeq) 202, 284
BSU29720 ytxE flagellar motor protein MotS (RefSeq) 48, 202
BSU29740 ccpA transcriptional regulator (Lacl family) (RefSeq) 63, 155
BSU31150 yubB undecaprenyl pyrophosphate phosphatase (RefSeq) 116, 155
BSU33260 yvrN putative ABC transporter (ATP-binding protein) (RefSeq) 125, 155
BSU33270 yvrO putative ABC transporter (ATP-binding protein) (RefSeq) 125, 155
BSU33280 yvrP putative ABC transporter component (RefSeq) 125, 155
BSU34710 yvcQ two-component sensor histidine kinase [YvcP] (RefSeq) 202, 325
BSU34800 cwlO secreted cell wall DL-endopeptidase (RefSeq) 155, 273
BSU35480 yviA hypothetical protein (RefSeq) 145, 155
BSU37330 argS arginyl-tRNA synthetase (RefSeq) 102, 155
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 BSU18850
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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