Organism : Bacillus cereus ATCC14579 | Module List :
BC2117

MoxR protein (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
MoxR-like ATPases cog/ cog
DNA binding go/ molecular_function
ATP binding go/ molecular_function
DNA-dependent DNA replication initiation go/ biological_process
DNA-dependent ATPase activity go/ molecular_function
magnesium chelatase activity go/ molecular_function
ATPase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2117
(Mouseover regulator name to see its description)

BC2117 is regulated by 21 influences and regulates 0 modules.
Regulators for BC2117 (21)
Regulator Module Operator
BC1477 193 tf
BC1531 193 tf
BC1537 193 tf
BC2133 193 tf
BC2551 193 tf
BC2672 193 tf
BC2815 193 tf
BC3756 193 tf
BC4277 193 tf
BC4525 193 tf
BC4842 193 tf
BC4968 193 tf
BC5200 193 tf
BC0042 179 tf
BC0840 179 tf
BC0848 179 tf
BC2358 179 tf
BC3690 179 tf
BC4091 179 tf
BC4170 179 tf
BC4703 179 tf

Warning: BC2117 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
4274 2.60e-05 AGGaGG
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4275 9.30e+03 CGgCTTgg
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4302 9.40e+00 GGAgGA
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4303 3.70e+01 TttCAC.TaCccTtttTTa
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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 BC2117

BC2117 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
MoxR-like ATPases cog/ cog
DNA binding go/ molecular_function
ATP binding go/ molecular_function
DNA-dependent DNA replication initiation go/ biological_process
DNA-dependent ATPase activity go/ molecular_function
magnesium chelatase activity go/ molecular_function
ATPase activity go/ molecular_function
Module neighborhood information for BC2117

BC2117 has total of 33 gene neighbors in modules 179, 193
Gene neighbors (33)
Gene Common Name Description Module membership
BC0333 BC0333 IMP cyclohydrolase (NCBI ptt file) 179, 416
BC1201 BC1201 None 76, 179
BC1215 BC1215 dTDP-4-dehydrorhamnose reductase (NCBI ptt file) 193, 240
BC1250 BC1250 hypothetical protein (NCBI ptt file) 179, 468
BC1478 BC1478 Sensor protein resE (NCBI ptt file) 193, 263
BC1575 BC1575 hypothetical protein (NCBI ptt file) 179, 484
BC1734 BC1734 Export ABC transporter ATP-binding protein (NCBI ptt file) 135, 193
BC2098 BC2098 hypothetical protein (NCBI ptt file) 179, 186
BC2107 BC2107 Quinone oxidoreductase (NCBI ptt file) 86, 179
BC2117 BC2117 MoxR protein (NCBI ptt file) 179, 193
BC2150 BC2150 metal-dependent phosphohydrolase (NCBI ptt file) 193, 417
BC2151 BC2151 ABC transporter ATP-binding protein uup (NCBI ptt file) 193, 417
BC2193 BC2193 MecA protein (NCBI ptt file) 193, 221
BC2294 BC2294 hypothetical Cytosolic Protein (NCBI ptt file) 193, 228
BC2295 BC2295 Exonuclease SbcD (NCBI ptt file) 41, 193
BC2296 BC2296 Exonuclease SbcC (NCBI ptt file) 141, 193
BC2328 BC2328 Pyruvate oxidase (NCBI ptt file) 96, 179
BC2923 BC2923 Acetyltransferase (NCBI ptt file) 193, 453
BC3192 BC3192 Protein ydhR precursor (NCBI ptt file) 179, 321
BC3409 BC3409 Transcriptional regulator, MarR family (NCBI ptt file) 31, 179
BC3756 BC3756 Transcriptional regulator, GntR family (NCBI ptt file) 193, 449
BC3768 BC3768 DNA mismatch repair protein mutL (NCBI ptt file) 193, 367
BC3769 BC3769 DNA mismatch repair protein mutS (NCBI ptt file) 118, 193
BC4042 BC4042 3-hydroxyisobutyrate dehydrogenase (NCBI ptt file) 193, 218
BC4164 BC4164 hypothetical protein (NCBI ptt file) 179, 506
BC4302 BC4302 PhoH protein (NCBI ptt file) 193, 417
BC4498 BC4498 ThiJ/PfpI family protein (NCBI ptt file) 108, 179
BC4569 BC4569 Multidrug resistance protein A (NCBI ptt file) 179, 285
BC4686 BC4686 Cell division protein ftsK (NCBI ptt file) 193, 451
BC5058 BC5058 Chloramphenicol resistance protein (NCBI ptt file) 179, 415
BC5200 BC5200 Transcriptional regulator, LytR family (NCBI ptt file) 193, 442
BC5245 BC5245 SWF/SNF family helicase (NCBI ptt file) 193, 243
BC5287 BC5287 Stage II sporulation protein D (NCBI ptt file) 193, 449
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 BC2117
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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