Organism : Bacillus cereus ATCC14579 | Module List :
BC4553

DNA polymerase X family (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
DNA polymerase IV (family X) cog/ cog
DNA-directed DNA polymerase activity go/ molecular_function
intracellular go/ cellular_component
DNA replication go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4553
(Mouseover regulator name to see its description)

BC4553 is regulated by 21 influences and regulates 0 modules.
Regulators for BC4553 (21)
Regulator Module Operator
BC0114 367 tf
BC0122 367 tf
BC0123 367 tf
BC1477 367 tf
BC1489 367 tf
BC1531 367 tf
BC2631 367 tf
BC3814 367 tf
BC3982 367 tf
BC4057 367 tf
BC4316 367 tf
BC4603 367 tf
BC5463 367 tf
BC3813 390 tf
BC3982 390 tf
BC4204 390 tf
BC4316 390 tf
BC5339 390 tf
BC5340 390 tf
BC5373 390 tf
BC5463 390 tf

Warning: BC4553 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
4644 1.50e+00 g.AtaaAaaAt.ggaAaaGAGGaG
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4645 6.10e+03 AAGGGG.Gac
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4690 5.00e-02 cAGaaaaaAcaA.ccga
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4691 1.90e+01 GACAaCTcAcCgGC
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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 BC4553

BC4553 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
DNA polymerase IV (family X) cog/ cog
DNA-directed DNA polymerase activity go/ molecular_function
intracellular go/ cellular_component
DNA replication go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for BC4553

BC4553 has total of 30 gene neighbors in modules 367, 390
Gene neighbors (30)
Gene Common Name Description Module membership
BC0003 BC0003 hypothetical protein (NCBI ptt file) 81, 390
BC0004 BC0004 DNA replication and repair protein recF (NCBI ptt file) 81, 390
BC1350 BC1350 hypothetical protein (NCBI ptt file) 390, 466
BC3768 BC3768 DNA mismatch repair protein mutL (NCBI ptt file) 193, 367
BC3780 BC3780 Competence-damage protein cinA (NCBI ptt file) 99, 367
BC3781 BC3781 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (NCBI ptt file) 99, 367
BC3782 BC3782 Transcriptional regulator (NCBI ptt file) 99, 367
BC3793 BC3793 Cell division protein ftsK (NCBI ptt file) 371, 390
BC3862 BC3862 Radical SAM family enzyme (NCBI ptt file) 367, 474
BC3863 BC3863 16S rRNA m(5)C 967 methyltransferase (NCBI ptt file) 94, 367
BC3864 BC3864 Methionyl-tRNA formyltransferase (NCBI ptt file) 94, 367
BC3867 BC3867 Phosphopantothenate-cysteine ligase (NCBI ptt file) 240, 367
BC3934 BC3934 Phosphoglycerate mutase (NCBI ptt file) 81, 390
BC3982 BC3982 Transcriptional regulators, LysR family (NCBI ptt file) 390, 433
BC4316 BC4316 Transcriptional regulator, MarR family (NCBI ptt file) 390, 527
BC4332 BC4332 GTP-binding protein (NCBI ptt file) 94, 367
BC4389 BC4389 Exodeoxyribonuclease V alpha chain (NCBI ptt file) 145, 367
BC4392 BC4392 Cysteine desulfhydrase (NCBI ptt file) 367, 474
BC4403 BC4403 Single-stranded-DNA-specific exonuclease recJ (NCBI ptt file) 79, 367
BC4415 BC4415 Holliday junction DNA helicase ruvA (NCBI ptt file) 390, 466
BC4553 BC4553 DNA polymerase X family (NCBI ptt file) 367, 390
BC4554 BC4554 Colicin V production protein (NCBI ptt file) 390, 466
BC4555 BC4555 hypothetical protein (NCBI ptt file) 390, 466
BC4556 BC4556 Ribonuclease HII (NCBI ptt file) 390, 466
BC4585 BC4585 Integral membrane protein (NCBI ptt file) 164, 367
BC4587 BC4587 DNA polymerase I (NCBI ptt file) 164, 367
BC5196 BC5196 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 260, 390
BC5244 BC5244 hypothetical Membrane Associated Protein (NCBI ptt file) 99, 367
BC5484 BC5484 Glucose inhibited division protein B (NCBI ptt file) 367, 374
BC5486 BC5486 Thiophene and furan oxidation protein ThdF (NCBI ptt file) 367, 374
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 BC4553
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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