Organism : Bacillus cereus ATCC14579 | Module List :
BC5385

Prespore specific transcriptional activator rsfA (NCBI ptt file)

CircVis
Functional Annotations (3)
Function System
DNA binding go/ molecular_function
nucleus go/ cellular_component
DNA_bind_RsfA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5385
(Mouseover regulator name to see its description)

BC5385 is regulated by 16 influences and regulates 1 modules.
Regulators for BC5385 (16)
Regulator Module Operator
BC0405 475 tf
BC1936 475 tf
BC2434 475 tf
BC2815 475 tf
BC4670 475 tf
BC5038 475 tf
BC5143 475 tf
BC5481 475 tf
BC2470 468 tf
BC2551 468 tf
BC3033 468 tf
BC3160 468 tf
BC4001 468 tf
BC4010 468 tf
BC4474 468 tf
BC5463 468 tf

Warning: BC5385 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
4846 1.40e+04 gaAtaGgaagt
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4847 3.10e+01 cgca.gAatGatgAGgggTt
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4860 1.50e+00 AaaGGgGA
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4861 2.30e+04 ggtAgaTTaaaAgggaAaGg
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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 BC5385

BC5385 is enriched for 3 functions in 4 categories.
Enrichment Table (3)
Function System
DNA binding go/ molecular_function
nucleus go/ cellular_component
DNA_bind_RsfA tigr/ tigrfam
Module neighborhood information for BC5385

BC5385 has total of 51 gene neighbors in modules 468, 475
Gene neighbors (51)
Gene Common Name Description Module membership
BC0168 BC0168 Mrp protein (NCBI ptt file) 194, 475
BC0236 BC0236 Transglycosylase (NCBI ptt file) 18, 475
BC0290 BC0290 ABC transporter ATP-binding protein uup (NCBI ptt file) 1, 475
BC0475 BC0475 None 97, 468
BC0498 BC0498 Regulatory protein recX (NCBI ptt file) 422, 475
BC0499 BC0499 Transcriptional regulator (NCBI ptt file) 48, 475
BC0562 BC0562 Ca2+/citrate complex secondary transporter (NCBI ptt file) 341, 468
BC0589 BC0589 Formate dehydrogenase alpha chain (NCBI ptt file) 48, 475
BC0595 BC0595 Cadmium efflux system accessory protein (NCBI ptt file) 335, 475
BC0596 BC0596 Zinc-transporting ATPase (NCBI ptt file) 335, 475
BC0630 BC0630 Trehalose operon transcriptional repressor (NCBI ptt file) 7, 475
BC0971 BC0971 Carboxylic ester hydrolase (NCBI ptt file) 250, 468
BC1163 BC1163 hypothetical Membrane Spanning Protein (NCBI ptt file) 228, 475
BC1245 BC1245 hypothetical protein (NCBI ptt file) 186, 468
BC1250 BC1250 hypothetical protein (NCBI ptt file) 179, 468
BC1462 BC1462 None 256, 468
BC1689 BC1689 hypothetical protein (NCBI ptt file) 166, 475
BC1711 BC1711 Short chain dehydrogenase (NCBI ptt file) 364, 475
BC1893 BC1893 Scaffold protein (NCBI ptt file) 141, 468
BC2321 BC2321 tRNA pseudouridine synthase A (NCBI ptt file) 10, 468
BC2402 BC2402 Tetracycline resistance protein (NCBI ptt file) 130, 468
BC2437 BC2437 hypothetical protein (NCBI ptt file) 28, 475
BC2555 BC2555 hypothetical protein (NCBI ptt file) 76, 468
BC2656 BC2656 Cobalt transport protein cbiQ (NCBI ptt file) 468, 506
BC2690 BC2690 Quaternary ammonium compound-resistance protein (NCBI ptt file) 443, 468
BC2843 BC2843 hypothetical protein (NCBI ptt file) 296, 475
BC3033 BC3033 Transcriptional regulator, AraC family (NCBI ptt file) 76, 468
BC3236 BC3236 hypothetical Cytosolic Protein (NCBI ptt file) 225, 468
BC3257 BC3257 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 134, 468
BC3438 BC3438 Transcriptional regulator, PadR family (NCBI ptt file) 353, 475
BC3602 BC3602 Anaerobic ribonucleoside-triphosphate reductase activating protein (NCBI ptt file) 175, 475
BC3616 BC3616 Aconitate hydratase (NCBI ptt file) 1, 475
BC3622 BC3622 Multidrug resistance protein B (NCBI ptt file) 263, 468
BC3755 BC3755 Murein hydrolase exporter (NCBI ptt file) 434, 475
BC3757 BC3757 hypothetical protein (NCBI ptt file) 430, 475
BC3990 BC3990 2,4-dienoyl-CoA reductase [NADPH] (NCBI ptt file) 434, 475
BC4086 BC4086 Purine nucleoside phosphorylase (NCBI ptt file) 28, 475
BC4087 BC4087 Phosphopentomutase (NCBI ptt file) 28, 475
BC4380 BC4380 hypothetical Cytosolic Protein (NCBI ptt file) 216, 475
BC4424 BC4424 Cysteine desulfhydrase (NCBI ptt file) 294, 475
BC4583 BC4583 NAD(P)-dependent glyceraldehyde-3-phosphate dehydrogenase (NCBI ptt file) 87, 475
BC4658 BC4658 Maltose O-acetyltransferase (NCBI ptt file) 264, 475
BC4829 BC4829 Ribosomal RNA adenine dimethylase (NCBI ptt file) 402, 468
BC4964 BC4964 hypothetical protein (NCBI ptt file) 434, 475
BC5172 BC5172 hypothetical protein (NCBI ptt file) 337, 475
BC5212 BC5212 None 31, 468
BC5225 BC5225 Cytochrome d ubiquinol oxidase subunit II (NCBI ptt file) 402, 468
BC5336 BC5336 Sporulation initiation phosphotransferase F (NCBI ptt file) 438, 475
BC5379 BC5379 dGTP triphosphohydrolase (NCBI ptt file) 414, 475
BC5385 BC5385 Prespore specific transcriptional activator rsfA (NCBI ptt file) 468, 475
BC5482 BC5482 Sporulation initiation inhibitor protein soj (NCBI ptt file) 434, 475
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 BC5385
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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