Organism : Bacillus subtilis | Module List :
BSU31040 yuaD

hypothetical protein (RefSeq)

CircVis
Functional Annotations (3)
Function System
catalytic activity go/ molecular_function
molybdenum ion binding go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BSU31040
(Mouseover regulator name to see its description)

BSU31040 is regulated by 22 influences and regulates 0 modules.
Regulators for BSU31040 yuaD (22)
Regulator Module Operator
BSU01430 61 tf
BSU04160 61 tf
BSU05850 61 tf
BSU06140 61 tf
BSU06960 61 tf
BSU09650 61 tf
BSU30260 61 tf
BSU31210 61 tf
BSU35910 61 tf
BSU38700 61 tf
BSU02550 334 tf
BSU04160 334 tf
BSU09330 334 tf
BSU09990 334 tf
BSU20820 334 tf
BSU24250 334 tf
BSU25760 334 tf
BSU34060 334 tf
BSU34180 334 tf
BSU35430 334 tf
BSU40960 334 tf
BSU40970 334 tf

Warning: BSU31040 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
5078 5.80e-07 aatgAAAaCGctTTC
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5079 4.10e+01 aCCccTcC
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5604 1.50e+03 ggAAa.GcaGA
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5605 2.00e+03 GGcATAAagTcaA.GaAgtgcg.G
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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 BSU31040

BSU31040 is enriched for 3 functions in 2 categories.
Enrichment Table (3)
Function System
catalytic activity go/ molecular_function
molybdenum ion binding go/ molecular_function
pyridoxal phosphate binding go/ molecular_function
Module neighborhood information for BSU31040

BSU31040 has total of 48 gene neighbors in modules 61, 334
Gene neighbors (48)
Gene Common Name Description Module membership
BSU04160 mtlR transcriptional regulator (RefSeq) 22, 61
BSU04390 ydbA hypothetical protein (RefSeq) 169, 334
BSU06160 gutP H+-glucitol symporter (RefSeq) 61, 326
BSU07800 treP phosphotransferase system (PTS) trehalose-specific enzyme IIBC component (RefSeq) 61, 321
BSU07810 treA trehalose-6-phosphate hydrolase (RefSeq) 61, 321
BSU12000 manR transcriptional antiterminator (RefSeq) 22, 61
BSU12010 manP phosphotransferase system (PTS) mannose-specific enzyme IIBCA component (RefSeq) 61, 168
BSU12020 manA mannose-6 phosphate isomerase ; cupin family (RefSeq) 22, 61
BSU14700 nprE extracellular neutral metalloprotease (RefSeq) 334, 353
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
BSU16750 asd aspartate-semialdehyde dehydrogenase (RefSeq) 155, 334
BSU17540 ynaF hypothetical protein (RefSeq) 81, 334
BSU18430 yogA putative oxidoreductase (RefSeq) 226, 334
BSU19220 yocI putative ATP-dependent nucleic acid helicase (RefSeq) 102, 334
BSU19520 yojA putative H+/anion permease (RefSeq) 61, 168
BSU22720 cheR methyl-accepting chemotaxis proteins (MCPs) methyltransferase (RefSeq) 102, 334
BSU23750 yqjT putative lyase (RefSeq) 102, 334
BSU24550 gcvPB glycine dehydrogenase subunit 2 (RefSeq) 169, 334
BSU24560 gcvPA glycine dehydrogenase subunit 1 (RefSeq) 229, 334
BSU24570 gcvT glycine cleavage system aminomethyltransferase T (RefSeq) 169, 334
BSU28730 araQ arabinose/arabinan permease (RefSeq) 61, 250
BSU28750 araN sugar-binding lipoprotein (RefSeq) 61, 250
BSU31040 yuaD hypothetical protein (RefSeq) 61, 334
BSU31180 yulE L-rhamnose isomerase (RefSeq) 61, 330
BSU31190 yulD L-rhamnose mutarotase (RefSeq) 61, 330
BSU31200 yulC rhamnulokinase (RefSeq) 61, 330
BSU31210 yulB putative transcriptional regulator (DeoR family) (RefSeq) 61, 330
BSU31670 yuxO putative esterase (RefSeq) 276, 334
BSU31720 degQ pleiotropic regulator (RefSeq) 61, 329
BSU34180 yvfI putative transcriptional regulator (GntR family) (RefSeq) 334, 393
BSU34950 pelC secreted pectate lyase (RefSeq) 52, 61
BSU35010 nagA N-acetylglucosamine-6-phosphate deacetylase (RefSeq) 334, 361
BSU35020 nagBA N-acetylglucosamine-6-phosphate isomerase (RefSeq) 334, 361
BSU35790 yvyI putative phosphohexomutase ; cupin family (RefSeq) 61, 248
BSU35870 pgsE factor required for polyglutamate synthesis (RefSeq) 44, 61
BSU35890 pgsC capsular polyglutamate amide ligase/translocase subunit (RefSeq) 61, 90
BSU35900 pgsB capsular polyglutamate synthetase (ATP-dependent amide ligase) (RefSeq) 61, 90
BSU36930 ywlE protein-tyrosine-phosphatase (RefSeq) 237, 334
BSU39020 yxjA purine nucleoside transporter (RefSeq) 309, 334
BSU39070 bglS endo-beta-1,3-1,4 glucanase (RefSeq) 61, 329
BSU40110 bglA aryl-6-phospho-beta-glucosidase (RefSeq) 61, 318
BSU40770 tetB multifunctional tetracycline-metal/H+ antiporter and Na+(K+)/H+ antiporter (RefSeq) 219, 334
BSU40780 tetL tetracycline resistance leader peptide (RefSeq) 219, 334
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 BSU31040
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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