Organism : Bacillus cereus ATCC14579 | Module List :
BC0945

DNA integration/recombination/invertion protein (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Site-specific recombinase XerD cog/ cog
DNA binding go/ molecular_function
DNA recombination go/ biological_process
DNA integration go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0945
(Mouseover regulator name to see its description)

BC0945 is regulated by 27 influences and regulates 0 modules.
Regulators for BC0945 (27)
Regulator Module Operator
BC0224 85 tf
BC0882 85 tf
BC0950 85 tf
BC2362 85 tf
BC2379 85 tf
BC2470 85 tf
BC2551 85 tf
BC2742 85 tf
BC3400 85 tf
BC3434 85 tf
BC3449 85 tf
BC3522 85 tf
BC3961 85 tf
BC4650 85 tf
BC5059 85 tf
BC0057 212 tf
BC0953 212 tf
BC1115 212 tf
BC1253 212 tf
BC2410 212 tf
BC2738 212 tf
BC3025 212 tf
BC3423 212 tf
BC3588 212 tf
BC4661 212 tf
BC4960 212 tf
BC5363 212 tf

Warning: BC0945 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
4088 1.60e+02 A.CaCCTctT
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4089 4.10e+04 GcCCATtTcaGCATcGaGG
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4340 6.50e-02 CTCCTTc
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4341 3.20e+04 AGGGcG
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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 BC0945

BC0945 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Site-specific recombinase XerD cog/ cog
DNA binding go/ molecular_function
DNA recombination go/ biological_process
DNA integration go/ biological_process
Module neighborhood information for BC0945

BC0945 has total of 62 gene neighbors in modules 85, 212
Gene neighbors (62)
Gene Common Name Description Module membership
BC0222 BC0222 Periplasmic molybdate-binding protein (NCBI ptt file) 85, 395
BC0268 BC0268 Zinc metalloprotease (NCBI ptt file) 212, 424
BC0358 BC0358 Quaternary ammonium compound-resistance protein (NCBI ptt file) 72, 85
BC0399 BC0399 Oxidoreductase (NCBI ptt file) 30, 85
BC0487 BC0487 UDP-N-acetyl-D-mannosamine 6-dehydrogenase (NCBI ptt file) 212, 376
BC0494 BC0494 hypothetical Cytosolic Protein (NCBI ptt file) 85, 139
BC0563 BC0563 Biotin carboxyl carrier protein (NCBI ptt file) 9, 85
BC0655 BC0655 Universal stress protein family (NCBI ptt file) 212, 454
BC0675 BC0675 hypothetical protein (NCBI ptt file) 85, 138
BC0771 BC0771 Protein erfK/srfK precursor (NCBI ptt file) 9, 85
BC0881 BC0881 Sensor protein comP (NCBI ptt file) 10, 85
BC0882 BC0882 Two-component response regulator comA (NCBI ptt file) 85, 453
BC0899 BC0899 hypothetical protein (NCBI ptt file) 85, 279
BC0923 BC0923 hypothetical protein (NCBI ptt file) 56, 85
BC0924 BC0924 hypothetical protein (NCBI ptt file) 85, 160
BC0929 BC0929 hypothetical protein (NCBI ptt file) 85, 279
BC0934 BC0934 hypothetical protein (NCBI ptt file) 9, 85
BC0944 BC0944 hypothetical protein (NCBI ptt file) 85, 279
BC0945 BC0945 DNA integration/recombination/invertion protein (NCBI ptt file) 85, 212
BC0950 BC0950 Transcriptional regulator, copG family (NCBI ptt file) 85, 146
BC0985 BC0985 hypothetical protein (NCBI ptt file) 85, 238
BC1073 BC1073 hypothetical protein (NCBI ptt file) 85, 163
BC1109 BC1109 hypothetical protein (NCBI ptt file) 85, 404
BC1255 BC1255 hypothetical protein (NCBI ptt file) 212, 216
BC1509 BC1509 Stage IV sporulation protein A (NCBI ptt file) 212, 437
BC1623 BC1623 Hfq protein (NCBI ptt file) 85, 97
BC1656 BC1656 Flagellin (NCBI ptt file) 30, 85
BC1660 BC1660 Soluble lytic murein transglycosylase (NCBI ptt file) 85, 424
BC1801 BC1801 Sensor protein vanS (NCBI ptt file) 212, 279
BC1848 BC1848 Prophage helix-turn-helix protein (NCBI ptt file) 9, 85
BC1935 BC1935 hypothetical protein (NCBI ptt file) 9, 85
BC2253 BC2253 hypothetical Cytosolic Protein (NCBI ptt file) 85, 154
BC2288 BC2288 Acyl-CoA dehydrogenase (NCBI ptt file) 212, 279
BC2289 BC2289 3-hydroxyisobutyrate dehydrogenase (NCBI ptt file) 212, 362
BC2290 BC2290 Methylmalonate-semialdehyde dehydrogenase (acylating) (NCBI ptt file) 212, 250
BC2362 BC2362 Transcriptional regulators, LysR family (NCBI ptt file) 30, 85
BC2379 BC2379 Transcriptional regulator (NCBI ptt file) 9, 85
BC2465 BC2465 hypothetical protein (NCBI ptt file) 85, 217
BC2470 BC2470 ECF-type sigma factor negative effector (NCBI ptt file) 85, 293
BC2474 BC2474 Ribosomal-protein-serine acetyltransferase (NCBI ptt file) 85, 248
BC2495 BC2495 hypothetical protein (NCBI ptt file) 85, 141
BC2552 BC2552 hypothetical protein (NCBI ptt file) 85, 171
BC2570 BC2570 Collagen triple helix repeat protein (NCBI ptt file) 85, 125
BC2622 BC2622 Macrolide glycosyltransferase (NCBI ptt file) 85, 250
BC2819 BC2819 hypothetical protein (NCBI ptt file) 85, 489
BC2961 BC2961 Sugar transport system permease protein (NCBI ptt file) 85, 158
BC3097 BC3097 Spore germination protein QC (NCBI ptt file) 24, 85
BC3106 BC3106 Small acid-soluble spore protein (NCBI ptt file) 54, 212
BC3138 BC3138 hypothetical protein (NCBI ptt file) 85, 364
BC3158 BC3158 Pyrimidine Reductase (NCBI ptt file) 34, 212
BC3232 BC3232 hypothetical protein (NCBI ptt file) 85, 364
BC3238 BC3238 hypothetical protein (NCBI ptt file) 85, 364
BC3425 BC3425 hypothetical Membrane Associated Protein (NCBI ptt file) 212, 424
BC3434 BC3434 Transcriptional regulator, DeoR family (NCBI ptt file) 9, 85
BC3610 BC3610 hypothetical protein (NCBI ptt file) 212, 364
BC3634 BC3634 Acetyltransferase (NCBI ptt file) 212, 279
BC3689 BC3689 Site-specific recombinase (NCBI ptt file) 85, 415
BC3714 BC3714 tRNA delta(2)-isopentenylpyrophosphate transferase (NCBI ptt file) 85, 308
BC3989 BC3989 Diguanylate cyclase/phosphodiesterase domain 2 (EAL) (NCBI ptt file) 72, 85
BC4945 BC4945 None 9, 85
BC5210 BC5210 PTS system, lichenan oligosaccharide-specific IIA component (NCBI ptt file) 212, 446
BC5403 BC5403 Integral membrane protein (NCBI ptt file) 85, 158
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 BC0945
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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