Organism : Bacillus cereus ATCC14579 | Module List :
BC2693

DNA polymerase III, beta chain (NCBI ptt file)

CircVis
Functional Annotations (12)
Function System
DNA polymerase sliding clamp subunit (PCNA homolog) cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA replication go/ biological_process
3'-5' exonuclease activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
dnan tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2693
(Mouseover regulator name to see its description)

BC2693 is regulated by 22 influences and regulates 0 modules.
Regulators for BC2693 (22)
Regulator Module Operator
BC0566 197 tf
BC0586 197 tf
BC1673 197 tf
BC1699 197 tf
BC1710 197 tf
BC2760 197 tf
BC3069 197 tf
BC3493 197 tf
BC3587 197 tf
BC3668 197 tf
BC4525 197 tf
BC4672 197 tf
BC0114 405 tf
BC0598 405 tf
BC1047 405 tf
BC2401 405 tf
BC3069 405 tf
BC3332 405 tf
BC3668 405 tf
BC4525 405 tf
BC4581 405 tf
BC4661 405 tf

Warning: BC2693 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
4310 1.30e+02 tgtAaGCGgttaC
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4311 1.40e+02 CtTtTTccatattT
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4720 1.90e-11 AaagGaGG
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4721 7.70e-02 aatattcAGAAaaTTcagttaaat
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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 BC2693

BC2693 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
DNA polymerase sliding clamp subunit (PCNA homolog) cog/ cog
DNA binding go/ molecular_function
DNA-directed DNA polymerase activity go/ molecular_function
DNA replication go/ biological_process
3'-5' exonuclease activity go/ molecular_function
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
DNA replication kegg/ kegg pathway
Mismatch repair kegg/ kegg pathway
Homologous recombination kegg/ kegg pathway
dnan tigr/ tigrfam
Module neighborhood information for BC2693

BC2693 has total of 50 gene neighbors in modules 197, 405
Gene neighbors (50)
Gene Common Name Description Module membership
BC0114 BC0114 RNA polymerase sigma-H factor (NCBI ptt file) 137, 405
BC0240 BC0240 hypothetical protein (NCBI ptt file) 123, 405
BC0373 BC0373 Na+/H+ antiporter NnaC (NCBI ptt file) 197, 199
BC0621 BC0621 2-amino-3-ketobutyrate coenzyme A ligase (NCBI ptt file) 197, 328
BC0622 BC0622 L-threonine 3-dehydrogenase (NCBI ptt file) 197, 328
BC0688 BC0688 Proline-specific permease (NCBI ptt file) 272, 405
BC0802 BC0802 Alcohol dehydrogenase (NCBI ptt file) 72, 197
BC0820 BC0820 Branched-chain amino acid transport system carrier protein (NCBI ptt file) 139, 197
BC0847 BC0847 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 340, 405
BC1157 BC1157 Alpha-amylase (NCBI ptt file) 405, 525
BC1239 BC1239 hypothetical Membrane Spanning Protein (NCBI ptt file) 405, 488
BC1263 BC1263 Phage integrase family protein (NCBI ptt file) 405, 517
BC1379 BC1379 Gentamicin resistance protein (NCBI ptt file) 364, 405
BC1523 BC1523 Menaquinol-cytochrome c reductase cytochrome b subunit (NCBI ptt file) 150, 405
BC1576 BC1576 Thiosulfate sulfurtransferase (NCBI ptt file) 197, 405
BC1749 BC1749 hypothetical protein (NCBI ptt file) 405, 495
BC1750 BC1750 hypothetical protein (NCBI ptt file) 405, 506
BC1751 BC1751 hypothetical protein (NCBI ptt file) 405, 495
BC1821 BC1821 Nucleoside permease nupC (NCBI ptt file) 197, 401
BC1836 BC1836 Branched-chain amino acid transport system carrier protein (NCBI ptt file) 405, 473
BC2047 BC2047 Branched-chain amino acid transport system carrier protein (NCBI ptt file) 213, 405
BC2291 BC2291 Transporter, LysE family (NCBI ptt file) 130, 405
BC2692 BC2692 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 141, 405
BC2693 BC2693 DNA polymerase III, beta chain (NCBI ptt file) 197, 405
BC2789 BC2789 hypothetical protein (NCBI ptt file) 405, 495
BC2973 BC2973 Nucleoside permease nupC (NCBI ptt file) 96, 197
BC3016 BC3016 hypothetical Membrane Spanning Protein (NCBI ptt file) 13, 197
BC3064 BC3064 Permease (NCBI ptt file) 282, 405
BC3185 BC3185 hypothetical protein (NCBI ptt file) 197, 199
BC3322 BC3322 hypothetical protein (NCBI ptt file) 197, 453
BC3367 BC3367 hypothetical protein (NCBI ptt file) 405, 434
BC3501 BC3501 Response regulator aspartate phosphatase (NCBI ptt file) 175, 197
BC3526 BC3526 Collagen adhesion protein (NCBI ptt file) 248, 405
BC3655 BC3655 Methyltransferase (NCBI ptt file) 197, 389
BC3700 BC3700 Phage protein (NCBI ptt file) 30, 197
BC3941 BC3941 Cytochrome c oxidase polypeptide IVB (NCBI ptt file) 357, 405
BC3942 BC3942 Cytochrome c oxidase polypeptide III (NCBI ptt file) 357, 405
BC3965 BC3965 hypothetical protein (NCBI ptt file) 197, 417
BC4060 BC4060 RibT protein (NCBI ptt file) 197, 446
BC4071 BC4071 Sodium/proline symporter (NCBI ptt file) 321, 405
BC4288 BC4288 Membrane-attached cytochrome c550 (NCBI ptt file) 358, 405
BC4550 BC4550 Threonine transporter (NCBI ptt file) 379, 405
BC4609 BC4609 hypothetical Membrane Spanning Protein (NCBI ptt file) 158, 405
BC4718 BC4718 Molybdopterin (MPT) converting factor, subunit 1 (NCBI ptt file) 241, 405
BC4767 BC4767 hypothetical protein (NCBI ptt file) 218, 405
BC4768 BC4768 NIF3-related protein (NCBI ptt file) 23, 405
BC5253 BC5253 ABC transporter permease protein (NCBI ptt file) 327, 405
BC5255 BC5255 periplasmic component of efflux system (NCBI ptt file) 327, 405
BC5415 BC5415 hypothetical Cytosolic Protein (NCBI ptt file) 23, 405
BC5439 BC5439 Murein hydrolase exporter (NCBI ptt file) 197, 199
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 BC2693
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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