Organism : Bacillus cereus ATCC14579 | Module List :
BC1477

Transcriptional regulatory protein resD (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1477
(Mouseover regulator name to see its description)

BC1477 is regulated by 25 influences and regulates 25 modules.
Regulators for BC1477 (25)
Regulator Module Operator
BC0057 117 tf
BC1477 117 tf
BC1489 117 tf
BC1680 117 tf
BC2903 117 tf
BC3493 117 tf
BC3904 117 tf
BC4336 117 tf
BC4589 117 tf
BC4603 117 tf
BC4672 117 tf
BC5176 117 tf
BC0613 417 tf
BC0657 417 tf
BC0659 417 tf
BC1477 417 tf
BC1531 417 tf
BC3332 417 tf
BC3690 417 tf
BC3844 417 tf
BC4211 417 tf
BC4294 417 tf
BC4314 417 tf
BC4336 417 tf
BC4650 417 tf

Warning: BC1477 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
4150 2.30e+02 aaAaGGaGcg
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4151 4.50e+02 GAGGaG
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4744 1.40e-05 cttAtTgtaaCcgcc.cgc.tT.t
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4745 1.60e-01 acaccTagtgtatgGgcggACAaG
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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 BC1477

BC1477 is enriched for 6 functions in 3 categories.
Module neighborhood information for BC1477

BC1477 has total of 34 gene neighbors in modules 117, 417
Gene neighbors (34)
Gene Common Name Description Module membership
BC0056 BC0056 Peptidyl-tRNA hydrolase (NCBI ptt file) 117, 243
BC0267 BC0267 Transcription accessory protein (S1 RNA binding domain) (NCBI ptt file) 22, 117
BC0659 BC0659 Ribose operon repressor (NCBI ptt file) 417, 524
BC0660 BC0660 Ribokinase (NCBI ptt file) 417, 524
BC0661 BC0661 High affinity ribose transport protein rbsD (NCBI ptt file) 417, 524
BC0662 BC0662 Ribose transport ATP-binding protein rbsA (NCBI ptt file) 417, 524
BC0663 BC0663 Ribose transport system permease protein rbsC (NCBI ptt file) 104, 417
BC1051 BC1051 Protein ecsB (NCBI ptt file) 117, 208
BC1477 BC1477 Transcriptional regulatory protein resD (NCBI ptt file) 117, 417
BC1544 BC1544 hypothetical protein (NCBI ptt file) 308, 417
BC1545 BC1545 hypothetical protein (NCBI ptt file) 308, 417
BC1572 BC1572 putative GTPases (dynamin-related) (NCBI ptt file) 417, 451
BC2008 BC2008 hypothetical protein (NCBI ptt file) 117, 304
BC2149 BC2149 hypothetical protein (NCBI ptt file) 334, 417
BC2150 BC2150 metal-dependent phosphohydrolase (NCBI ptt file) 193, 417
BC2151 BC2151 ABC transporter ATP-binding protein uup (NCBI ptt file) 193, 417
BC2201 BC2201 Outer membrane protein romA (NCBI ptt file) 117, 273
BC3203 BC3203 hypothetical Exported Protein (NCBI ptt file) 234, 417
BC3499 BC3499 hypothetical Cytosolic Protein (NCBI ptt file) 117, 394
BC3771 BC3771 IG hypothetical 16757 (NCBI ptt file) 22, 117
BC3964 BC3964 hypothetical protein (NCBI ptt file) 417, 485
BC3965 BC3965 hypothetical protein (NCBI ptt file) 197, 417
BC3966 BC3966 hypothetical protein (NCBI ptt file) 417, 485
BC3979 BC3979 Cytochrome d ubiquinol oxidase subunit II (NCBI ptt file) 117, 527
BC4177 BC4177 Dimethylallyltransferase (NCBI ptt file) 22, 417
BC4302 BC4302 PhoH protein (NCBI ptt file) 193, 417
BC4560 BC4560 Phenylalanyl-tRNA synthetase beta chain (NCBI ptt file) 412, 417
BC4561 BC4561 Phenylalanyl-tRNA synthetase alpha chain (NCBI ptt file) 412, 417
BC4685 BC4685 Nicotinate phosphoribosyltransferase (NCBI ptt file) 22, 417
BC4940 BC4940 ABC transporter ATP-binding protein (NCBI ptt file) 117, 273
BC5376 BC5376 hypothetical Cytosolic Protein (NCBI ptt file) 117, 126
BC5377 BC5377 Membrane metalloprotease (NCBI ptt file) 117, 235
BC5430 BC5430 Oligosaccharide translocase (flippase) (NCBI ptt file) 117, 145
BC5461 BC5461 hypothetical membrane protein yycH (NCBI ptt file) 117, 374
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 BC1477
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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