Organism : Bacillus cereus ATCC14579 | Module List :
BC4297

GTP-binding protein (NCBI ptt file)

CircVis
Functional Annotations (10)
Function System
GTPase cog/ cog
RNA binding go/ molecular_function
GTPase activity go/ molecular_function
GTP binding go/ molecular_function
intracellular go/ cellular_component
Gram-negative-bacterium-type cell wall go/ cellular_component
ferrous iron transmembrane transporter activity go/ molecular_function
ferrous iron transport go/ biological_process
integral to membrane go/ cellular_component
small_GTP tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4297
(Mouseover regulator name to see its description)

BC4297 is regulated by 26 influences and regulates 0 modules.
Regulators for BC4297 (26)
Regulator Module Operator
BC0051 371 tf
BC0116 371 tf
BC0158 371 tf
BC1531 371 tf
BC3128 371 tf
BC3332 371 tf
BC3814 371 tf
BC3976 371 tf
BC4181 371 tf
BC4294 371 tf
BC4570 371 tf
BC4603 371 tf
BC4670 371 tf
BC0586 273 tf
BC0648 273 tf
BC1329 273 tf
BC1477 273 tf
BC1710 273 tf
BC1719 273 tf
BC1818 273 tf
BC2988 273 tf
BC3976 273 tf
BC4001 273 tf
BC4672 273 tf
BC5339 273 tf
BC5373 273 tf

Warning: BC4297 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
4462 2.30e+00 ga.AgGagggg
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4463 3.10e+04 GtCGaTGAGcC
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4652 7.70e+01 GaAGgGg
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4653 1.10e+00 AGcAaaAAggAggg
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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 BC4297

BC4297 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
GTPase cog/ cog
RNA binding go/ molecular_function
GTPase activity go/ molecular_function
GTP binding go/ molecular_function
intracellular go/ cellular_component
Gram-negative-bacterium-type cell wall go/ cellular_component
ferrous iron transmembrane transporter activity go/ molecular_function
ferrous iron transport go/ biological_process
integral to membrane go/ cellular_component
small_GTP tigr/ tigrfam
Module neighborhood information for BC4297

BC4297 has total of 34 gene neighbors in modules 273, 371
Gene neighbors (34)
Gene Common Name Description Module membership
BC0043 BC0043 Methionyl-tRNA synthetase (NCBI ptt file) 273, 296
BC0071 BC0071 Hypoxanthine-guanine phosphoribosyltransferase (NCBI ptt file) 273, 439
BC0493 BC0493 1,2-diacylglycerol 3-glucosyltransferase (NCBI ptt file) 81, 273
BC1512 BC1512 Heptaprenyl diphosphate synthase component I (NCBI ptt file) 260, 273
BC1710 BC1710 Transcriptional regulator, MerR family (NCBI ptt file) 273, 507
BC1719 BC1719 Transcriptional regulator, MecI family (NCBI ptt file) 15, 273
BC1818 BC1818 Transcriptional regulator, TetR family (NCBI ptt file) 6, 273
BC1826 BC1826 CcdC protein (NCBI ptt file) 118, 273
BC2044 BC2044 Magnesium and cobalt efflux protein corC (NCBI ptt file) 110, 273
BC2201 BC2201 Outer membrane protein romA (NCBI ptt file) 117, 273
BC3774 BC3774 Pyruvate synthase alpha chain (NCBI ptt file) 371, 455
BC3793 BC3793 Cell division protein ftsK (NCBI ptt file) 371, 390
BC3797 BC3797 Dihydrodipicolinate synthase (NCBI ptt file) 371, 474
BC3798 BC3798 Aspartokinase (NCBI ptt file) 371, 426
BC3799 BC3799 Aspartate-semialdehyde dehydrogenase (NCBI ptt file) 371, 426
BC3807 BC3807 Riboflavin kinase (NCBI ptt file) 71, 371
BC3808 BC3808 tRNA pseudouridine synthase B (NCBI ptt file) 71, 371
BC3854 BC3854 Predicted kinase related to hydroxyacetone kinase (NCBI ptt file) 260, 371
BC3855 BC3855 putative alkaline-shock protein (NCBI ptt file) 371, 447
BC3976 BC3976 putative transcriptional regulator (NCBI ptt file) 326, 371
BC4089 BC4089 DNA integration/recombination/invertion protein (NCBI ptt file) 273, 447
BC4090 BC4090 hypothetical protein (NCBI ptt file) 273, 447
BC4180 BC4180 Methylenetetrahydrofolate dehydrogenase (NADP+) (NCBI ptt file) 371, 450
BC4278 BC4278 High-affinity zinc uptake system membrane protein znuB (NCBI ptt file) 169, 371
BC4292 BC4292 EMG2 protein (NCBI ptt file) 371, 447
BC4293 BC4293 hypothetical Cytosolic Protein (NCBI ptt file) 371, 455
BC4294 BC4294 CBS domain containing protein (NCBI ptt file) 371, 455
BC4297 BC4297 GTP-binding protein (NCBI ptt file) 273, 371
BC4298 BC4298 Cytidine deaminase (NCBI ptt file) 71, 371
BC4321 BC4321 DNA polymerase III, delta subunit (NCBI ptt file) 41, 273
BC4758 BC4758 Molybdenum cofactor biosynthesis protein B (NCBI ptt file) 119, 273
BC4936 BC4936 Diaminopimelate epimerase (NCBI ptt file) 119, 273
BC4940 BC4940 ABC transporter ATP-binding protein (NCBI ptt file) 117, 273
BC5165 BC5165 Integral membrane protein (NCBI ptt file) 74, 273
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 BC4297
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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