Organism : Bacillus cereus ATCC14579 | Module List :
BC3342

hypothetical Membrane Spanning Protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted permease cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3342
(Mouseover regulator name to see its description)

BC3342 is regulated by 28 influences and regulates 0 modules.
Regulators for BC3342 (28)
Regulator Module Operator
BC0613 506 tf
BC1302 506 tf
BC2351 506 tf
BC2766 506 tf
BC2794 506 tf
BC2903 506 tf
BC3039 506 tf
BC4256 506 tf
BC4433 506 tf
BC4570 506 tf
BC4661 506 tf
BC4670 506 tf
BC0213 389 tf
BC0499 389 tf
BC0851 389 tf
BC1969 389 tf
BC2410 389 tf
BC2551 389 tf
BC3025 389 tf
BC3253 389 tf
BC3592 389 tf
BC3702 389 tf
BC3983 389 tf
BC4076 389 tf
BC4101 389 tf
BC4356 389 tf
BC4930 389 tf
BC5175 389 tf

Warning: BC3342 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
4688 3.80e+01 GGtGGa
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4689 6.00e+03 aaagaTAAacatGaaAAaGgag
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4922 7.00e+02 CCG.CAcgAcATGagtCc
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4923 2.60e+03 aGgAaGggGgaag
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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 BC3342

BC3342 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted permease cog/ cog
Module neighborhood information for BC3342

BC3342 has total of 25 gene neighbors in modules 389, 506
Gene neighbors (25)
Gene Common Name Description Module membership
BC0314 BC0314 Glycosyltransferase (NCBI ptt file) 9, 506
BC0502 BC0502 hypothetical Cytosolic Protein (NCBI ptt file) 266, 389
BC0786 BC0786 Nitroreductase family (NCBI ptt file) 389, 443
BC0851 BC0851 Mercuric resistance operon regulatory protein (NCBI ptt file) 389, 449
BC1126 BC1126 S-layer homology domain (NCBI ptt file) 213, 506
BC1750 BC1750 hypothetical protein (NCBI ptt file) 405, 506
BC2034 BC2034 Export protein for polysaccharides and teichoic acids (NCBI ptt file) 230, 506
BC2176 BC2176 1,3-propanediol dehydrogenase (NCBI ptt file) 294, 389
BC2208 BC2208 Iron(III) dicitrate-binding protein (NCBI ptt file) 389, 416
BC2219 BC2219 Phenazine biosynthesis protein phzF (NCBI ptt file) 96, 506
BC2604 BC2604 hypothetical Membrane Spanning Protein (NCBI ptt file) 263, 389
BC2656 BC2656 Cobalt transport protein cbiQ (NCBI ptt file) 468, 506
BC2765 BC2765 hypothetical protein (NCBI ptt file) 415, 506
BC3211 BC3211 NADPH-cytochrome P450 reductase (NCBI ptt file) 484, 506
BC3278 BC3278 hypothetical protein (NCBI ptt file) 26, 506
BC3342 BC3342 hypothetical Membrane Spanning Protein (NCBI ptt file) 389, 506
BC3577 BC3577 Amino acid permease (NCBI ptt file) 389, 443
BC3655 BC3655 Methyltransferase (NCBI ptt file) 197, 389
BC3759 BC3759 6-phospho-beta-glucosidase (NCBI ptt file) 165, 506
BC3983 BC3983 CBS domain containing protein (NCBI ptt file) 308, 389
BC4164 BC4164 hypothetical protein (NCBI ptt file) 179, 506
BC4537 BC4537 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 376, 506
BC4927 BC4927 Cell surface protein (NCBI ptt file) 130, 506
BC5350 BC5350 Transcriptional activator plcR (NCBI ptt file) 139, 506
BC5381 BC5381 Ferrichrome transport ATP-binding protein fhuC (NCBI ptt file) 389, 443
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 BC3342
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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