Organism : Bacillus cereus ATCC14579 | Module List :
BC4181

N utilization substance protein B (NCBI ptt file)

CircVis
Functional Annotations (6)
Function System
Transcription termination factor cog/ cog
transcription termination factor activity go/ molecular_function
RNA binding go/ molecular_function
transcription termination, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
nusB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4181
(Mouseover regulator name to see its description)

BC4181 is regulated by 24 influences and regulates 19 modules.
Regulators for BC4181 (24)
Regulator Module Operator
BC0073 451 tf
BC1531 451 tf
BC1537 451 tf
BC2133 451 tf
BC3072 451 tf
BC3207 451 tf
BC3332 451 tf
BC3690 451 tf
BC3814 451 tf
BC4181 451 tf
BC5200 451 tf
BC5411 451 tf
BC5463 451 tf
BC0073 450 tf
BC1047 450 tf
BC1427 450 tf
BC1489 450 tf
BC1531 450 tf
BC3072 450 tf
BC3756 450 tf
BC3961 450 tf
BC4181 450 tf
BC4316 450 tf
BC5200 450 tf

Warning: BC4181 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
4810 7.30e-02 agtaggAgaAAGgGa
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4811 2.40e+03 AggagGGA
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4812 2.00e-03 CcCcCtatggcccag
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4813 1.20e+03 AggagGA..AaGgG
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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 BC4181

BC4181 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcription termination factor cog/ cog
transcription termination factor activity go/ molecular_function
RNA binding go/ molecular_function
transcription termination, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
nusB tigr/ tigrfam
Module neighborhood information for BC4181

BC4181 has total of 40 gene neighbors in modules 450, 451
Gene neighbors (40)
Gene Common Name Description Module membership
BC0186 BC0186 hypothetical Membrane Spanning Protein (NCBI ptt file) 450, 451
BC0187 BC0187 hypothetical Membrane Associated Protein (NCBI ptt file) 450, 451
BC0624 BC0624 von Willebrand factor type A domain protein (NCBI ptt file) 450, 451
BC0625 BC0625 NorQ protein (NCBI ptt file) 450, 451
BC1213 BC1213 dTDP-4-dehydrorhamnose 3,5-epimerase (NCBI ptt file) 240, 451
BC1214 BC1214 dTDP-glucose 4,6-dehydratase (NCBI ptt file) 240, 451
BC1485 BC1485 ATP-dependent DNA helicase recQ (NCBI ptt file) 268, 450
BC1486 BC1486 CAAX amino terminal protease family (NCBI ptt file) 268, 450
BC1488 BC1488 phosphoesterase (NCBI ptt file) 268, 450
BC1489 BC1489 Transcriptional regulator, MerR family (NCBI ptt file) 268, 450
BC1516 BC1516 Chorismate synthase (NCBI ptt file) 240, 451
BC1531 BC1531 hypothetical Transcriptional Regulatory Protein (NCBI ptt file) 439, 450
BC1532 BC1532 Dihydrodipicolinate reductase (NCBI ptt file) 450, 527
BC1533 BC1533 Methylglyoxal synthase (NCBI ptt file) 240, 450
BC1534 BC1534 Lmbe-related protein (NCBI ptt file) 240, 450
BC1535 BC1535 Glycosyltransferase (NCBI ptt file) 240, 450
BC1536 BC1536 Poly(A) polymerase (NCBI ptt file) 240, 450
BC1540 BC1540 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI ptt file) 329, 450
BC1541 BC1541 Pantoate--beta-alanine ligase (NCBI ptt file) 329, 450
BC1542 BC1542 Aspartate 1-decarboxylase (NCBI ptt file) 329, 450
BC1543 BC1543 None 385, 451
BC1572 BC1572 putative GTPases (dynamin-related) (NCBI ptt file) 417, 451
BC2293 BC2293 hypothetical protein (NCBI ptt file) 450, 511
BC3304 BC3304 hypothetical Membrane Spanning Protein (NCBI ptt file) 254, 451
BC3860 BC3860 Serine/threonine protein kinase (NCBI ptt file) 240, 451
BC3861 BC3861 Protein phosphatase 2C (NCBI ptt file) 240, 451
BC3920 BC3920 2-dehydropantoate 2-reductase (NCBI ptt file) 268, 450
BC3926 BC3926 ATP-dependent protease La (NCBI ptt file) 451, 518
BC3927 BC3927 Serine protease (NCBI ptt file) 451, 518
BC4176 BC4176 1-deoxy-D-xylulose 5-phosphate synthase (NCBI ptt file) 451, 518
BC4178 BC4178 Exodeoxyribonuclease VII small subunit (NCBI ptt file) 240, 451
BC4179 BC4179 Exodeoxyribonuclease VII large subunit (NCBI ptt file) 240, 451
BC4180 BC4180 Methylenetetrahydrofolate dehydrogenase (NADP+) (NCBI ptt file) 371, 450
BC4181 BC4181 N utilization substance protein B (NCBI ptt file) 450, 451
BC4580 BC4580 Replication initiation and membrane attachment protein (NCBI ptt file) 252, 450
BC4605 BC4605 DNA polymerase III alpha subunit (NCBI ptt file) 268, 450
BC4686 BC4686 Cell division protein ftsK (NCBI ptt file) 193, 451
BC4850 BC4850 None 329, 451
BC4854 BC4854 Menaquinone biosynthesis related protein (NCBI ptt file) 451, 467
BC5160 BC5160 TPR-repeat-containing protein (NCBI ptt file) 242, 451
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 BC4181
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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