Organism : Bacillus cereus ATCC14579 | Module List :
BC3405

Transcriptional regulator, GntR family (NCBI ptt file)

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

Cytoscape Web
Regulation information for BC3405
(Mouseover regulator name to see its description)

BC3405 is regulated by 31 influences and regulates 17 modules.
Regulators for BC3405 (31)
Regulator Module Operator
BC0059 313 tf
BC0123 313 tf
BC0785 313 tf
BC1080 313 tf
BC1449 313 tf
BC3062 313 tf
BC3405 313 tf
BC3438 313 tf
BC3592 313 tf
BC3690 313 tf
BC3702 313 tf
BC3813 313 tf
BC3814 313 tf
BC4661 313 tf
BC4902 313 tf
BC5205 313 tf
BC0099 481 tf
BC0410 481 tf
BC0595 481 tf
BC0851 481 tf
BC1302 481 tf
BC2122 481 tf
BC2218 481 tf
BC3095 481 tf
BC3253 481 tf
BC3706 481 tf
BC3826 481 tf
BC3922 481 tf
BC4072 481 tf
BC4708 481 tf
BC5402 481 tf

Warning: BC3405 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
4540 1.60e+02 ccaCcGCGCGGaAGaGG
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4541 6.80e+01 ctCCttcttT
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4872 2.80e+03 CGCGCC
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4873 1.10e+04 AgaaAcaAgGgGGAg
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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 BC3405

BC3405 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
transcription regulator activity go/ molecular_function
Module neighborhood information for BC3405

BC3405 has total of 41 gene neighbors in modules 313, 481
Gene neighbors (41)
Gene Common Name Description Module membership
BC0334 BC0334 Phosphoribosylamine--glycine ligase (NCBI ptt file) 313, 354
BC0354 BC0354 Phosphoglycolate phosphatase (NCBI ptt file) 431, 481
BC0470 BC0470 S-layer protein / N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 382, 481
BC0678 BC0678 Methyl-accepting chemotaxis protein (NCBI ptt file) 396, 481
BC1156 BC1156 Ammonium transporter (NCBI ptt file) 214, 481
BC1344 BC1344 GTP cyclohydrolase I (NCBI ptt file) 192, 313
BC1384 BC1384 Bacitracin resistance protein (Putative undecaprenol kinase) (NCBI ptt file) 382, 481
BC1577 BC1577 hypothetical protein (NCBI ptt file) 428, 481
BC1612 BC1612 Na+/H+ antiporter NapA (inosine-dependent germination) (NCBI ptt file) 88, 481
BC1932 BC1932 Transcriptional regulators, LysR family (NCBI ptt file) 97, 481
BC1938 BC1938 Cytochrome d ubiquinol oxidase subunit I (NCBI ptt file) 429, 481
BC1941 BC1941 Transport ATP-binding protein cydC (NCBI ptt file) 429, 481
BC2398 BC2398 putative integral membrane protein (NCBI ptt file) 100, 481
BC2619 BC2619 Sporulation kinase (NCBI ptt file) 465, 481
BC2830 BC2830 DNA-binding protein (NCBI ptt file) 72, 481
BC2880 BC2880 Multidrug resistance protein B (NCBI ptt file) 161, 481
BC3124 BC3124 Isochorismatase family (NCBI ptt file) 218, 313
BC3398 BC3398 Serine transporter (NCBI ptt file) 214, 481
BC3405 BC3405 Transcriptional regulator, GntR family (NCBI ptt file) 313, 481
BC3406 BC3406 Oxidoreductase (NCBI ptt file) 313, 481
BC3435 BC3435 Daunorubicin resistance transmembrane protein (NCBI ptt file) 313, 461
BC3437 BC3437 hypothetical Cytosolic Protein (NCBI ptt file) 313, 337
BC3507 BC3507 hypothetical protein (NCBI ptt file) 428, 481
BC3662 BC3662 Cytochrome c-type biogenesis protein ccdA (NCBI ptt file) 290, 481
BC3719 BC3719 1-phosphofructokinase (NCBI ptt file) 234, 481
BC3776 BC3776 Stage V sporulation protein S (NCBI ptt file) 76, 481
BC4454 BC4454 hypothetical protein (NCBI ptt file) 313, 337
BC4455 BC4455 IG hypothetical 17788 (NCBI ptt file) 313, 493
BC4456 BC4456 Type I restriction-modification system restriction subunit (NCBI ptt file) 313, 493
BC4457 BC4457 Type I restriction-modification system restriction subunit (NCBI ptt file) 313, 493
BC4458 BC4458 Type I restriction-modification system specificity subunit (NCBI ptt file) 313, 493
BC4459 BC4459 Type I restriction-modification system methylation subunit (NCBI ptt file) 313, 493
BC4460 BC4460 Type I restriction-modification system specificity subunit (NCBI ptt file) 313, 493
BC4494 BC4494 Ribonuclease PH (NCBI ptt file) 313, 357
BC4688 BC4688 hypothetical protein (NCBI ptt file) 257, 313
BC4944 BC4944 hypothetical protein (NCBI ptt file) 214, 481
BC5033 BC5033 None 224, 481
BC5187 BC5187 Cytochrome c551 (NCBI ptt file) 7, 481
BC5207 BC5207 Chromate transport protein (NCBI ptt file) 431, 481
BC5357 BC5357 Collagen adhesion protein (NCBI ptt file) 88, 313
BC5358 BC5358 Collagen adhesion protein (NCBI ptt file) 431, 481
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 BC3405
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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