Organism : Bacillus cereus ATCC14579 | Module List :
BC0498

Regulatory protein recX (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
regulation of DNA repair go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0498
(Mouseover regulator name to see its description)

BC0498 is regulated by 23 influences and regulates 6 modules.
Regulators for BC0498 (23)
Regulator Module Operator
BC0498 422 tf
BC0680 422 tf
BC1080 422 tf
BC1695 422 tf
BC1841 422 tf
BC2672 422 tf
BC2738 422 tf
BC3062 422 tf
BC3356 422 tf
BC3813 422 tf
BC4072 422 tf
BC4652 422 tf
BC4703 422 tf
BC5038 422 tf
BC5481 422 tf
BC0405 475 tf
BC1936 475 tf
BC2434 475 tf
BC2815 475 tf
BC4670 475 tf
BC5038 475 tf
BC5143 475 tf
BC5481 475 tf

Warning: BC0498 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
4754 2.30e-01 AgAaAagGgta
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4755 5.60e+01 caaGaGGAa.accaAgTggttTcg
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4860 1.50e+00 AaaGGgGA
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4861 2.30e+04 ggtAgaTTaaaAgggaAaGg
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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 BC0498

BC0498 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
regulation of DNA repair go/ biological_process
Module neighborhood information for BC0498

BC0498 has total of 53 gene neighbors in modules 422, 475
Gene neighbors (53)
Gene Common Name Description Module membership
BC0053 BC0053 Stage V sporulation protein G (NCBI ptt file) 216, 422
BC0168 BC0168 Mrp protein (NCBI ptt file) 194, 475
BC0236 BC0236 Transglycosylase (NCBI ptt file) 18, 475
BC0290 BC0290 ABC transporter ATP-binding protein uup (NCBI ptt file) 1, 475
BC0498 BC0498 Regulatory protein recX (NCBI ptt file) 422, 475
BC0499 BC0499 Transcriptional regulator (NCBI ptt file) 48, 475
BC0540 BC0540 Mutator mutT protein (7,8-dihydro-8-oxoguanine-triphosphatase) (NCBI ptt file) 422, 491
BC0589 BC0589 Formate dehydrogenase alpha chain (NCBI ptt file) 48, 475
BC0595 BC0595 Cadmium efflux system accessory protein (NCBI ptt file) 335, 475
BC0596 BC0596 Zinc-transporting ATPase (NCBI ptt file) 335, 475
BC0630 BC0630 Trehalose operon transcriptional repressor (NCBI ptt file) 7, 475
BC0972 BC0972 hypothetical protein (NCBI ptt file) 211, 422
BC0982 BC0982 hypothetical protein (NCBI ptt file) 333, 422
BC1163 BC1163 hypothetical Membrane Spanning Protein (NCBI ptt file) 228, 475
BC1605 BC1605 Transporter, LysE family (NCBI ptt file) 333, 422
BC1606 BC1606 hypothetical Cytosolic Protein (NCBI ptt file) 211, 422
BC1689 BC1689 hypothetical protein (NCBI ptt file) 166, 475
BC1692 BC1692 hypothetical protein (NCBI ptt file) 173, 422
BC1711 BC1711 Short chain dehydrogenase (NCBI ptt file) 364, 475
BC1771 BC1771 Fibronectin-binding protein (NCBI ptt file) 294, 422
BC1915 BC1915 Transcriptional regulator, PBSX family (NCBI ptt file) 203, 422
BC2235 BC2235 hypothetical protein (NCBI ptt file) 203, 422
BC2437 BC2437 hypothetical protein (NCBI ptt file) 28, 475
BC2843 BC2843 hypothetical protein (NCBI ptt file) 296, 475
BC3438 BC3438 Transcriptional regulator, PadR family (NCBI ptt file) 353, 475
BC3602 BC3602 Anaerobic ribonucleoside-triphosphate reductase activating protein (NCBI ptt file) 175, 475
BC3616 BC3616 Aconitate hydratase (NCBI ptt file) 1, 475
BC3755 BC3755 Murein hydrolase exporter (NCBI ptt file) 434, 475
BC3757 BC3757 hypothetical protein (NCBI ptt file) 430, 475
BC3880 BC3880 hypothetical Membrane Spanning Protein (NCBI ptt file) 333, 422
BC3881 BC3881 Phosphoglycolate phosphatase (NCBI ptt file) 333, 422
BC3990 BC3990 2,4-dienoyl-CoA reductase [NADPH] (NCBI ptt file) 434, 475
BC4086 BC4086 Purine nucleoside phosphorylase (NCBI ptt file) 28, 475
BC4087 BC4087 Phosphopentomutase (NCBI ptt file) 28, 475
BC4167 BC4167 Glycerophosphoryl diester phosphodiesterase (NCBI ptt file) 129, 422
BC4380 BC4380 hypothetical Cytosolic Protein (NCBI ptt file) 216, 475
BC4424 BC4424 Cysteine desulfhydrase (NCBI ptt file) 294, 475
BC4583 BC4583 NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) 87, 475
BC4652 BC4652 Transcriptional regulator IcaR (NCBI ptt file) 173, 422
BC4658 BC4658 Maltose O-acetyltransferase (NCBI ptt file) 264, 475
BC4754 BC4754 putative acetyltransferase/acyltransferase (NCBI ptt file) 129, 422
BC4776 BC4776 hypothetical protein (NCBI ptt file) 216, 422
BC4964 BC4964 hypothetical protein (NCBI ptt file) 434, 475
BC4971 BC4971 Phosphoglycerate mutase (NCBI ptt file) 73, 422
BC4972 BC4972 DNA-binding protein (NCBI ptt file) 73, 422
BC4993 BC4993 hypothetical lipoprotein (NCBI ptt file) 333, 422
BC5011 BC5011 hypothetical protein (NCBI ptt file) 422, 440
BC5172 BC5172 hypothetical protein (NCBI ptt file) 337, 475
BC5336 BC5336 Sporulation initiation phosphotransferase F (NCBI ptt file) 438, 475
BC5379 BC5379 dGTP triphosphohydrolase (NCBI ptt file) 414, 475
BC5385 BC5385 Prespore specific transcriptional activator rsfA (NCBI ptt file) 468, 475
BC5417 BC5417 Two-component response regulator (NCBI ptt file) 422, 473
BC5482 BC5482 Sporulation initiation inhibitor protein soj (NCBI ptt file) 434, 475
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 BC0498
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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