Organism : Bacillus cereus ATCC14579 | Module List :
BC1253

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 BC1253
(Mouseover regulator name to see its description)

BC1253 is regulated by 29 influences and regulates 6 modules.
Regulators for BC1253 (29)
Regulator Module Operator
BC0123 279 tf
BC0224 279 tf
BC0356 279 tf
BC0953 279 tf
BC1698 279 tf
BC2217 279 tf
BC2526 279 tf
BC2738 279 tf
BC2914 279 tf
BC3449 279 tf
BC3493 279 tf
BC3589 279 tf
BC4212 279 tf
BC4277 279 tf
BC4960 279 tf
BC0123 316 tf
BC0601 316 tf
BC0953 316 tf
BC0958 316 tf
BC0961 316 tf
BC1047 316 tf
BC1134 316 tf
BC2526 316 tf
BC2738 316 tf
BC2766 316 tf
BC3244 316 tf
BC3493 316 tf
BC4661 316 tf
BC4960 316 tf

Warning: BC1253 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
4474 7.60e-01 AaaAtagGggg
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4475 5.50e+03 AgaagAAatGg
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4546 2.30e-05 AGgGGagG.aAa
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4547 6.20e-01 tTtt.ggaAggaggg
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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 BC1253

BC1253 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 BC1253

BC1253 has total of 58 gene neighbors in modules 279, 316
Gene neighbors (58)
Gene Common Name Description Module membership
BC0356 BC0356 Sigma-54-dependent transcriptional activator (NCBI ptt file) 279, 525
BC0890 BC0890 Long-chain-fatty-acid--CoA ligase (NCBI ptt file) 146, 279
BC0899 BC0899 hypothetical protein (NCBI ptt file) 85, 279
BC0919 BC0919 hypothetical protein (NCBI ptt file) 279, 425
BC0929 BC0929 hypothetical protein (NCBI ptt file) 85, 279
BC0930 BC0930 hypothetical protein (NCBI ptt file) 248, 279
BC0931 BC0931 hypothetical Membrane Spanning Protein (NCBI ptt file) 248, 279
BC0944 BC0944 hypothetical protein (NCBI ptt file) 85, 279
BC0952 BC0952 hypothetical protein (NCBI ptt file) 316, 454
BC0958 BC0958 Transcriptional regulator (NCBI ptt file) 284, 316
BC1158 BC1158 Transcriptional regulator, XRE family (NCBI ptt file) 316, 391
BC1253 BC1253 Transcriptional regulator, PBSX family (NCBI ptt file) 279, 316
BC1261 BC1261 ATP/GTP-binding protein (NCBI ptt file) 238, 316
BC1262 BC1262 hypothetical protein (NCBI ptt file) 238, 316
BC1801 BC1801 Sensor protein vanS (NCBI ptt file) 212, 279
BC2077 BC2077 hypothetical protein (NCBI ptt file) 316, 464
BC2174 BC2174 Phosphoglycolate phosphatase (NCBI ptt file) 72, 316
BC2216 BC2216 Two-component sensor protein yhcY (NCBI ptt file) 279, 424
BC2217 BC2217 Two-component response regulator yhcZ (NCBI ptt file) 218, 279
BC2286 BC2286 2-methylisocitrate dehydratase (NCBI ptt file) 279, 355
BC2288 BC2288 Acyl-CoA dehydrogenase (NCBI ptt file) 212, 279
BC2299 BC2299 hypothetical protein (NCBI ptt file) 299, 316
BC2314 BC2314 hypothetical protein (NCBI ptt file) 238, 316
BC2421 BC2421 DNA integration/recombination/invertion protein (NCBI ptt file) 316, 464
BC2585 BC2585 Portal protein (NCBI ptt file) 7, 316
BC2708 BC2708 hypothetical Cytosolic Protein (NCBI ptt file) 279, 395
BC2709 BC2709 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 163, 279
BC2750 BC2750 hypothetical protein (NCBI ptt file) 20, 279
BC2827 BC2827 Chitin binding protein (NCBI ptt file) 316, 478
BC2869 BC2869 N-acetylglucosaminyldiphosphoundecaprenol N-acetyl-beta-D-mannosaminyltransferase (NCBI ptt file) 279, 524
BC3221 BC3221 surface protein (NCBI ptt file) 224, 316
BC3231 BC3231 Microcin C7 self-immunity protein mccF (NCBI ptt file) 279, 409
BC3244 BC3244 Leucine-responsive regulatory protein (NCBI ptt file) 316, 381
BC3245 BC3245 Amino acid permease (NCBI ptt file) 316, 415
BC3261 BC3261 hypothetical protein (NCBI ptt file) 30, 279
BC3271 BC3271 hypothetical protein (NCBI ptt file) 316, 381
BC3364 BC3364 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 316, 381
BC3420 BC3420 NAD(P)H oxidoreductase YRKL (NCBI ptt file) 316, 381
BC3634 BC3634 Acetyltransferase (NCBI ptt file) 212, 279
BC3694 BC3694 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 30, 279
BC3695 BC3695 holin (NCBI ptt file) 30, 279
BC3696 BC3696 XpaF1 protein (NCBI ptt file) 279, 424
BC3698 BC3698 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 30, 279
BC3699 BC3699 Antigen (NCBI ptt file) 30, 279
BC3984 BC3984 hypothetical protein (NCBI ptt file) 163, 316
BC4007 BC4007 Sporulation kinase B (NCBI ptt file) 264, 316
BC4043 BC4043 Penicillin-binding protein (NCBI ptt file) 279, 469
BC4223 BC4223 hypothetical protein (NCBI ptt file) 72, 279
BC4234 BC4234 ComG operon protein 7 (NCBI ptt file) 279, 359
BC4538 BC4538 Two-component sensor kinase ycbM (NCBI ptt file) 248, 316
BC4539 BC4539 Two-component response regulator ycbL (NCBI ptt file) 163, 316
BC4619 BC4619 hypothetical protein (NCBI ptt file) 30, 316
BC4620 BC4620 Zwittermicin A resistance protein zmaR (NCBI ptt file) 248, 316
BC4621 BC4621 hypothetical protein (NCBI ptt file) 279, 316
BC4622 BC4622 hypothetical protein (NCBI ptt file) 316, 454
BC4665 BC4665 Two-component response regulator (NCBI ptt file) 238, 316
BC4824 BC4824 ABC transporter ATP-binding protein (NCBI ptt file) 2, 279
BC4931 BC4931 hypothetical Cytosolic Protein (NCBI ptt file) 20, 316
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 BC1253
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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