Organism : Bacillus cereus ATCC14579 | Module List :
BC3987

NRDH-redoxin (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
Glutaredoxin and related proteins cog/ cog
electron carrier activity go/ molecular_function
protein disulfide oxidoreductase activity go/ molecular_function
cell redox homeostasis go/ biological_process
GlrX_YruB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3987
(Mouseover regulator name to see its description)

BC3987 is regulated by 22 influences and regulates 0 modules.
Regulators for BC3987 (22)
Regulator Module Operator
BC2358 103 tf
BC3758 103 tf
BC4240 103 tf
BC4256 103 tf
BC4672 103 tf
BC5265 103 tf
BC5332 103 tf
BC0595 477 tf
BC0607 477 tf
BC0880 477 tf
BC1077 477 tf
BC1131 477 tf
BC3095 477 tf
BC3868 477 tf
BC4174 477 tf
BC4256 477 tf
BC4708 477 tf
BC4826 477 tf
BC5010 477 tf
BC5024 477 tf
BC5339 477 tf
BC5402 477 tf

Warning: BC3987 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
4122 6.80e+02 gAAAaaaGgaG
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4123 1.30e+03 ATGaGAaGG
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4864 9.40e-01 AtAaaaacAag.aggaAa.
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4865 9.90e-02 cgcCtt.TctCtTTTtaAtcattt
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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 BC3987

BC3987 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Glutaredoxin and related proteins cog/ cog
electron carrier activity go/ molecular_function
protein disulfide oxidoreductase activity go/ molecular_function
cell redox homeostasis go/ biological_process
GlrX_YruB tigr/ tigrfam
Module neighborhood information for BC3987

BC3987 has total of 39 gene neighbors in modules 103, 477
Gene neighbors (39)
Gene Common Name Description Module membership
BC0205 BC0205 hypothetical protein (NCBI ptt file) 7, 477
BC0336 BC0336 Somatin-like protein (NCBI ptt file) 103, 337
BC0435 BC0435 Transcriptional regulator, PBSX family (NCBI ptt file) 103, 443
BC0482 BC0482 PTS system, N-acetylglucosamine-specific IIBC component (NCBI ptt file) 103, 290
BC0892 BC0892 hypothetical protein (NCBI ptt file) 399, 477
BC1131 BC1131 Cold shock protein (NCBI ptt file) 187, 477
BC1172 BC1172 ComZ protein (NCBI ptt file) 20, 477
BC1481 BC1481 hypothetical protein (NCBI ptt file) 147, 477
BC1615 BC1615 Na+ driven multidrug efflux pump (NCBI ptt file) 92, 103
BC1926 BC1926 Low-affinity zinc transport protein (NCBI ptt file) 103, 478
BC2204 BC2204 Asparagine synthetase [glutamine-hydrolyzing] (NCBI ptt file) 474, 477
BC2357 BC2357 Cold shock protein (NCBI ptt file) 198, 477
BC3095 BC3095 Ans operon repressor protein (NCBI ptt file) 147, 477
BC3758 BC3758 Transcriptional regulator, GntR family (NCBI ptt file) 103, 430
BC3925 BC3925 None 103, 247
BC3956 BC3956 GTP-binding protein TypA/BipA (NCBI ptt file) 382, 477
BC3957 BC3957 hypothetical protein (NCBI ptt file) 350, 477
BC3981 BC3981 Tetrahydrodipicolinate N-acetyltransferase (NCBI ptt file) 103, 399
BC3987 BC3987 NRDH-redoxin (NCBI ptt file) 103, 477
BC4062 BC4062 IG hypothetical 17221 (NCBI ptt file) 100, 477
BC4081 BC4081 Transcriptional regulator, MarR family (NCBI ptt file) 246, 477
BC4201 BC4201 hypothetical Membrane Spanning Protein (NCBI ptt file) 103, 298
BC4202 BC4202 hypothetical Membrane Spanning Protein (NCBI ptt file) 103, 298
BC4370 BC4370 hypothetical protein (NCBI ptt file) 100, 477
BC4540 BC4540 hypothetical protein (NCBI ptt file) 442, 477
BC4693 BC4693 Deblocking aminopeptidase (NCBI ptt file) 103, 385
BC4870 BC4870 L-lactate dehydrogenase (NCBI ptt file) 167, 477
BC4906 BC4906 Aspartate aminotransferase (NCBI ptt file) 15, 477
BC4914 BC4914 None 103, 401
BC4917 BC4917 BioY protein (NCBI ptt file) 103, 350
BC4958 BC4958 NAD(P)H dehydrogenase [quinone] (NCBI ptt file) 103, 414
BC5018 BC5018 hypothetical Membrane Spanning Protein (NCBI ptt file) 265, 477
BC5052 BC5052 None 103, 126
BC5256 BC5256 Transcriptional regulator, PBSX family (NCBI ptt file) 103, 245
BC5317 BC5317 hypothetical protein (NCBI ptt file) 28, 103
BC5318 BC5318 Ribose 5-phosphate isomerase (NCBI ptt file) 103, 385
BC5386 BC5386 Lipoate-protein ligase A (NCBI ptt file) 198, 477
BC5396 BC5396 hydrolase (HAD superfamily) (NCBI ptt file) 103, 126
BC5468 BC5468 Adenylosuccinate synthetase (NCBI ptt file) 290, 477
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 BC3987
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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