Organism : Bacillus cereus ATCC14579 | Module List :
BC0769

Guanine-hypoxanthine permease (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Permeases cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0769
(Mouseover regulator name to see its description)

BC0769 is regulated by 32 influences and regulates 0 modules.
Regulators for BC0769 (32)
Regulator Module Operator
BC0099 8 tf
BC0116 8 tf
BC0607 8 tf
BC0954 8 tf
BC1622 8 tf
BC1889 8 tf
BC2181 8 tf
BC2770 8 tf
BC3095 8 tf
BC3207 8 tf
BC3400 8 tf
BC3449 8 tf
BC4010 8 tf
BC4057 8 tf
BC4499 8 tf
BC4650 8 tf
BC5000 8 tf
BC5339 8 tf
BC0099 62 tf
BC0116 62 tf
BC0975 62 tf
BC1363 62 tf
BC1841 62 tf
BC2401 62 tf
BC3095 62 tf
BC3826 62 tf
BC3922 62 tf
BC3961 62 tf
BC4057 62 tf
BC4525 62 tf
BC4650 62 tf
BC5402 62 tf

Warning: BC0769 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
3938 2.80e+03 AtGAtAgGAA
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3939 1.20e+02 ccTttctaTTT
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4044 1.30e+01 GGAgGA
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4045 6.70e+01 CcCTTTttctTTTgG
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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 BC0769

BC0769 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Permeases cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
Module neighborhood information for BC0769

BC0769 has total of 40 gene neighbors in modules 8, 62
Gene neighbors (40)
Gene Common Name Description Module membership
BC0369 BC0369 Zinc metalloprotease (NCBI ptt file) 8, 364
BC0604 BC0604 hypothetical Exported Protein (NCBI ptt file) 62, 308
BC0677 BC0677 Bacitracin resistance protein (Putative undecaprenol kinase) (NCBI ptt file) 8, 147
BC0769 BC0769 Guanine-hypoxanthine permease (NCBI ptt file) 8, 62
BC0812 BC0812 PBS lyase HEAT-like repeat (NCBI ptt file) 62, 256
BC0894 BC0894 Polysaccharides export protein (NCBI ptt file) 8, 75
BC1259 BC1259 hypothetical protein (NCBI ptt file) 62, 214
BC1527 BC1527 hypothetical protein (NCBI ptt file) 62, 176
BC1595 BC1595 hypothetical protein (NCBI ptt file) 8, 62
BC1599 BC1599 hypothetical Membrane Spanning Protein (NCBI ptt file) 8, 37
BC1622 BC1622 Stage 0 sporulation regulatory protein (NCBI ptt file) 8, 97
BC1632 BC1632 Chemotaxis protein methyltransferase (NCBI ptt file) 8, 147
BC1633 BC1633 hypothetical protein (NCBI ptt file) 8, 147
BC2033 BC2033 Alkaline phosphatase like protein (NCBI ptt file) 8, 341
BC2059 BC2059 Phosphoglycerate mutase (NCBI ptt file) 62, 428
BC2060 BC2060 hydrolase (HAD superfamily) (NCBI ptt file) 62, 428
BC2497 BC2497 Sensor protein vanS (NCBI ptt file) 8, 147
BC2498 BC2498 Two-component response regulator vanR (NCBI ptt file) 8, 147
BC2557 BC2557 Prophage helix-turn-helix protein (NCBI ptt file) 62, 256
BC2713 BC2713 UvrC-like protein (NCBI ptt file) 62, 396
BC2763 BC2763 hypothetical Cytosolic Protein (NCBI ptt file) 8, 62
BC2771 BC2771 hypothetical Exported Protein (NCBI ptt file) 62, 213
BC3195 BC3195 hypothetical Cytosolic Protein (NCBI ptt file) 62, 341
BC3457 BC3457 hypothetical protein (NCBI ptt file) 62, 453
BC3528 BC3528 Sporulation kinase (NCBI ptt file) 8, 55
BC3538 BC3538 DNA polymerase III, epsilon chain (NCBI ptt file) 62, 308
BC3777 BC3777 IG hypothetical 15594 (NCBI ptt file) 62, 222
BC4056 BC4056 ComE operon protein 3 (NCBI ptt file) 62, 222
BC4080 BC4080 hypothetical protein (NCBI ptt file) 8, 62
BC4138 BC4138 Metal-dependent hydrolase (NCBI ptt file) 8, 37
BC4453 BC4453 Phage protein (NCBI ptt file) 62, 440
BC4638 BC4638 Adenine-specific methyltransferase (NCBI ptt file) 62, 222
BC4696 BC4696 SAM-dependent methyltransferase (NCBI ptt file) 8, 176
BC4939 BC4939 Stage 0 sporulation regulatory protein (NCBI ptt file) 10, 62
BC4942 BC4942 PhnA protein (NCBI ptt file) 62, 382
BC5005 BC5005 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 8, 147
BC5050 BC5050 Nucleoside permease nupC (NCBI ptt file) 8, 147
BC5242 BC5242 Membrane protein with C2C2 zinc finger (NCBI ptt file) 62, 204
BC5450 BC5450 hypothetical Cytosolic Protein (NCBI ptt file) 8, 147
BC5451 BC5451 ATP-dependent RNA helicase (NCBI ptt file) 8, 75
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 BC0769
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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