Organism : Bacillus cereus ATCC14579 | Module List :
BC3693

Transcriptional regulator, PadR family (NCBI ptt file)

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

Cytoscape Web
Regulation information for BC3693
(Mouseover regulator name to see its description)

BC3693 is regulated by 30 influences and regulates 5 modules.
Regulators for BC3693 (30)
Regulator Module Operator
BC0851 402 tf
BC1603 402 tf
BC2386 402 tf
BC2442 402 tf
BC2988 402 tf
BC3084 402 tf
BC3095 402 tf
BC3253 402 tf
BC3421 402 tf
BC3434 402 tf
BC3693 402 tf
BC3720 402 tf
BC4165 402 tf
BC4174 402 tf
BC4703 402 tf
BC4930 402 tf
BC5175 402 tf
BC5250 402 tf
BC0477 385 tf
BC0648 385 tf
BC0758 385 tf
BC0840 385 tf
BC1053 385 tf
BC1814 385 tf
BC2480 385 tf
BC3332 385 tf
BC3792 385 tf
BC4073 385 tf
BC4181 385 tf
BC5200 385 tf

Warning: BC3693 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
4680 5.10e+01 AaCCtCCtcaC.tAtgTG.G
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4681 8.70e+02 T.AGcagaCaaaAataaaaAaagA
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4714 8.30e-02 Ata.CAGaaAAgAaGGGGAgT
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4715 1.80e+01 gCaat.cctgCacCT
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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 BC3693

BC3693 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulators cog/ cog
Module neighborhood information for BC3693

BC3693 has total of 39 gene neighbors in modules 385, 402
Gene neighbors (39)
Gene Common Name Description Module membership
BC0617 BC0617 None 134, 385
BC0776 BC0776 Sucrose operon repressor (NCBI ptt file) 246, 385
BC0886 BC0886 hydrolase (HAD superfamily) (NCBI ptt file) 25, 402
BC1294 BC1294 hypothetical Membrane Spanning Protein (NCBI ptt file) 385, 449
BC1543 BC1543 None 385, 451
BC1920 BC1920 Phage protein (NCBI ptt file) 361, 402
BC1989 BC1989 hypothetical Membrane Spanning Protein (NCBI ptt file) 284, 402
BC1991 BC1991 putative murein endopeptidase (NCBI ptt file) 171, 385
BC2460 BC2460 Succinoglycan biosynthesis protein (NCBI ptt file) 31, 402
BC2480 BC2480 Transcriptional regulator, TetR family (NCBI ptt file) 385, 480
BC2756 BC2756 6-aminohexanoate-dimer hydrolase (NCBI ptt file) 265, 402
BC2978 BC2978 Peptidase family M20 (NCBI ptt file) 359, 402
BC3390 BC3390 Nitroreductase family protein (NCBI ptt file) 52, 402
BC3394 BC3394 4-oxalocrotonate tautomerase (NCBI ptt file) 31, 402
BC3546 BC3546 Cell surface protein (NCBI ptt file) 15, 385
BC3547 BC3547 Cell surface protein (NCBI ptt file) 127, 385
BC3693 BC3693 Transcriptional regulator, PadR family (NCBI ptt file) 385, 402
BC3935 BC3935 hypothetical Cytosolic Protein (NCBI ptt file) 402, 414
BC3936 BC3936 hypothetical Cytosolic Protein (NCBI ptt file) 56, 402
BC3940 BC3940 CtaG protein (NCBI ptt file) 385, 479
BC3980 BC3980 putative N-acetyldiaminopimelate deacetylase (NCBI ptt file) 127, 385
BC4055 BC4055 N-acetylgalactosamine-6-phosphate deacetylase (NCBI ptt file) 18, 385
BC4323 BC4323 ComE operon protein 2 (NCBI ptt file) 261, 385
BC4432 BC4432 Two-component sensor kinase yvcQ (NCBI ptt file) 163, 385
BC4467 BC4467 Stage VI sporulation protein D (NCBI ptt file) 59, 402
BC4481 BC4481 TPR repeat protein (NCBI ptt file) 329, 385
BC4693 BC4693 Deblocking aminopeptidase (NCBI ptt file) 103, 385
BC4726 BC4726 hypothetical protein (NCBI ptt file) 385, 414
BC4727 BC4727 hypothetical protein (NCBI ptt file) 41, 385
BC4825 BC4825 ABC transporter ATP-binding protein (NCBI ptt file) 141, 385
BC4829 BC4829 Ribosomal RNA adenine dimethylase (NCBI ptt file) 402, 468
BC4988 BC4988 hypothetical protein (NCBI ptt file) 385, 438
BC5060 BC5060 hypothetical protein (NCBI ptt file) 385, 430
BC5061 BC5061 NADH dehydrogenase (NCBI ptt file) 385, 480
BC5164 BC5164 HPR(SER) kinase (NCBI ptt file) 385, 482
BC5199 BC5199 Xaa-Pro dipeptidase (NCBI ptt file) 261, 385
BC5225 BC5225 Cytochrome d ubiquinol oxidase subunit II (NCBI ptt file) 402, 468
BC5318 BC5318 Ribose 5-phosphate isomerase (NCBI ptt file) 103, 385
BC5418 BC5418 Transporter, MFS superfamily (NCBI ptt file) 385, 414
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 BC3693
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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