Organism : Bacillus cereus ATCC14579 | Module List :
BC3332

Transcriptional regulator, PBSX family (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3332
(Mouseover regulator name to see its description)

BC3332 is regulated by 20 influences and regulates 34 modules.
Regulators for BC3332 (20)
Regulator Module Operator
BC0477 272 tf
BC1851 272 tf
BC2680 272 tf
BC2964 272 tf
BC3332 272 tf
BC3982 272 tf
BC4336 272 tf
BC0122 248 tf
BC0598 248 tf
BC0680 248 tf
BC1531 248 tf
BC2178 248 tf
BC2410 248 tf
BC3244 248 tf
BC3332 248 tf
BC3449 248 tf
BC3493 248 tf
BC3589 248 tf
BC4960 248 tf
BC5074 248 tf

Warning: BC3332 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
4412 5.90e+00 gtaaaAaGggtg.Atag
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4413 2.00e+04 Tc.GgAGG
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4460 3.70e-12 aAGGGGg
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4461 2.20e+04 GGACGcAC
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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 BC3332

BC3332 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BC3332

BC3332 has total of 46 gene neighbors in modules 248, 272
Gene neighbors (46)
Gene Common Name Description Module membership
BC0261 BC0261 hypothetical membrane protein (Rhomboid family) (NCBI ptt file) 272, 415
BC0308 BC0308 Glycosyltransferase (NCBI ptt file) 272, 487
BC0309 BC0309 Methyltransferase (NCBI ptt file) 272, 339
BC0310 BC0310 Methyltransferase (NCBI ptt file) 272, 487
BC0411 BC0411 hypothetical protein (NCBI ptt file) 72, 248
BC0477 BC0477 Transcriptional regulator (NCBI ptt file) 272, 459
BC0620 BC0620 Ubiquinone/menaquinone biosynthesis methyltransferase UBIE (NCBI ptt file) 199, 248
BC0650 BC0650 Pyrimidine Reductase (NCBI ptt file) 248, 267
BC0680 BC0680 Transcriptional regulator, PBSX family (NCBI ptt file) 184, 248
BC0688 BC0688 Proline-specific permease (NCBI ptt file) 272, 405
BC0714 BC0714 Acriflavin resistance plasma membrane protein (NCBI ptt file) 248, 272
BC0861 BC0861 hypothetical protein (NCBI ptt file) 272, 378
BC0930 BC0930 hypothetical protein (NCBI ptt file) 248, 279
BC0931 BC0931 hypothetical Membrane Spanning Protein (NCBI ptt file) 248, 279
BC1249 BC1249 hypothetical Cytosolic Protein (NCBI ptt file) 181, 272
BC1397 BC1397 None 272, 282
BC1442 BC1442 hypothetical protein (NCBI ptt file) 248, 454
BC1445 BC1445 hypothetical protein (NCBI ptt file) 186, 272
BC1640 BC1640 hypothetical protein (NCBI ptt file) 155, 248
BC1894 BC1894 Phage protein (NCBI ptt file) 272, 334
BC2255 BC2255 hypothetical protein (NCBI ptt file) 272, 340
BC2383 BC2383 Oxalate decarboxylase (NCBI ptt file) 272, 334
BC2474 BC2474 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 85, 248
BC2477 BC2477 hypothetical protein (NCBI ptt file) 196, 272
BC2518 BC2518 Methyltransferase (NCBI ptt file) 248, 454
BC2683 BC2683 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 104, 272
BC2734 BC2734 Pullulanase (NCBI ptt file) 248, 352
BC2816 BC2816 hypothetical protein (NCBI ptt file) 174, 272
BC2825 BC2825 hypothetical protein (NCBI ptt file) 248, 454
BC3329 BC3329 ABC transporter ATP-binding protein (NCBI ptt file) 248, 363
BC3332 BC3332 Transcriptional regulator, PBSX family (NCBI ptt file) 248, 272
BC3470 BC3470 hypothetical protein (NCBI ptt file) 248, 363
BC3492 BC3492 Permease (NCBI ptt file) 248, 294
BC3526 BC3526 Collagen adhesion protein (NCBI ptt file) 248, 405
BC3725 BC3725 Exochitinase (NCBI ptt file) 272, 289
BC4196 BC4196 hypothetical protein (NCBI ptt file) 248, 381
BC4304 BC4304 hypothetical Cytosolic Protein (NCBI ptt file) 217, 272
BC4409 BC4409 hypothetical protein (NCBI ptt file) 128, 272
BC4513 BC4513 Chemotaxis motA protein (NCBI ptt file) 248, 489
BC4538 BC4538 Two-component sensor kinase ycbM (NCBI ptt file) 248, 316
BC4620 BC4620 Zwittermicin A resistance protein zmaR (NCBI ptt file) 248, 316
BC4764 BC4764 hypothetical protein (NCBI ptt file) 272, 378
BC4783 BC4783 hydrolase (HAD superfamily) (NCBI ptt file) 130, 248
BC5116 BC5116 hypothetical protein (NCBI ptt file) 34, 248
BC5147 BC5147 Stage V sporulation protein AC (NCBI ptt file) 102, 272
BC5480 BC5480 hypothetical protein (NCBI ptt file) 131, 272
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 BC3332
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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