Organism : Bacillus cereus ATCC14579 | Module List :
BC5402

Transcriptional regulator, LacI family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5402
(Mouseover regulator name to see its description)

BC5402 is regulated by 31 influences and regulates 33 modules.
Regulators for BC5402 (31)
Regulator Module Operator
BC0073 237 tf
BC0356 237 tf
BC0598 237 tf
BC1427 237 tf
BC1489 237 tf
BC1537 237 tf
BC2122 237 tf
BC2794 237 tf
BC3826 237 tf
BC3922 237 tf
BC4081 237 tf
BC4174 237 tf
BC4968 237 tf
BC5402 237 tf
BC5434 237 tf
BC0082 365 tf
BC0598 365 tf
BC1427 365 tf
BC1537 365 tf
BC2549 365 tf
BC2794 365 tf
BC2971 365 tf
BC3069 365 tf
BC3826 365 tf
BC3922 365 tf
BC4834 365 tf
BC4968 365 tf
BC5191 365 tf
BC5265 365 tf
BC5402 365 tf
BC5434 365 tf

Warning: BC5402 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
4390 2.80e-01 AGGggagaaa.
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4391 1.70e+02 cGCAaAAAggG
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4640 1.40e+02 AAGgGGaaAaTGA
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4641 1.90e+03 CCaAtgaCGcg
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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 BC5402

BC5402 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for BC5402

BC5402 has total of 28 gene neighbors in modules 237, 365
Gene neighbors (28)
Gene Common Name Description Module membership
BC0936 BC0936 Two-component sensor kinase citS (NCBI ptt file) 237, 365
BC0937 BC0937 Two-component response regulator citT (NCBI ptt file) 237, 365
BC0938 BC0938 Tricarboxylate-binding protein (NCBI ptt file) 237, 365
BC1762 BC1762 Fosmidomycin resistance protein (NCBI ptt file) 237, 365
BC1763 BC1763 Cysteine synthase (NCBI ptt file) 237, 365
BC1764 BC1764 Acetyltransferase (NCBI ptt file) 237, 365
BC1765 BC1765 hypothetical Cytosolic Protein (NCBI ptt file) 237, 365
BC1766 BC1766 hypothetical protein (NCBI ptt file) 237, 365
BC1921 BC1921 Site-specific recombinase (NCBI ptt file) 237, 359
BC1922 BC1922 Glutamyl-tRNA(Gln) amidotransferase subunit A (NCBI ptt file) 237, 359
BC2548 BC2548 Homoserine dehydrogenase (NCBI ptt file) 365, 377
BC2549 BC2549 Transcriptional regulator, GntR family (NCBI ptt file) 365, 375
BC3045 BC3045 hypothetical Membrane Spanning Protein (NCBI ptt file) 105, 237
BC3048 BC3048 Aminoglycoside phosphotransferase (NCBI ptt file) 237, 365
BC3049 BC3049 hypothetical Cytosolic Protein (NCBI ptt file) 237, 365
BC4719 BC4719 Molybdopterin (MPT) converting factor, subunit 2 (NCBI ptt file) 237, 365
BC4720 BC4720 Molybdopterin-guanine dinucleotide biosynthesis protein B (NCBI ptt file) 237, 365
BC4721 BC4721 Molybdopterin biosynthesis MoeA protein (NCBI ptt file) 237, 365
BC4724 BC4724 Molybdenum cofactor biosynthesis protein A (NCBI ptt file) 237, 258
BC4863 BC4863 Glycogen phosphorylase (NCBI ptt file) 98, 365
BC4864 BC4864 Glycogen synthase (NCBI ptt file) 237, 365
BC4865 BC4865 None 112, 365
BC4866 BC4866 Glucose-1-phosphate adenylyltransferase (NCBI ptt file) 237, 365
BC4867 BC4867 1,4-alpha-glucan branching enzyme (NCBI ptt file) 237, 365
BC5398 BC5398 Uracil-DNA glycosylase (NCBI ptt file) 105, 237
BC5399 BC5399 Bacitracin transport permease protein BCRB (NCBI ptt file) 237, 287
BC5400 BC5400 Bacitracin transport ATP-binding protein bcrA (NCBI ptt file) 237, 286
BC5402 BC5402 Transcriptional regulator, LacI family (NCBI ptt file) 237, 365
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 BC5402
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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