Organism : Bacillus cereus ATCC14579 | Module List :
BC5483

Stage 0 sporulation protein J (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
plasmid partitioning go/ biological_process
parB_part tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC5483
(Mouseover regulator name to see its description)

BC5483 is regulated by 26 influences and regulates 8 modules.
Regulators for BC5483 (26)
Regulator Module Operator
BC0880 126 tf
BC1282 126 tf
BC1998 126 tf
BC3389 126 tf
BC3522 126 tf
BC4170 126 tf
BC4672 126 tf
BC4826 126 tf
BC5010 126 tf
BC5339 126 tf
BC5402 126 tf
BC5483 126 tf
BC0051 275 tf
BC0116 275 tf
BC1282 275 tf
BC2166 275 tf
BC3814 275 tf
BC3868 275 tf
BC3976 275 tf
BC4170 275 tf
BC4204 275 tf
BC4289 275 tf
BC4316 275 tf
BC5332 275 tf
BC5339 275 tf
BC5483 275 tf

Warning: BC5483 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
4168 4.00e+02 TcAtcTccTcttttc
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4169 3.20e+03 GCGGCtG
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4466 3.60e+02 gAgGTGaaA
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4467 5.70e+03 CCctTGTTGGTAAG
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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 BC5483

BC5483 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulators cog/ cog
DNA binding go/ molecular_function
plasmid partitioning go/ biological_process
parB_part tigr/ tigrfam
Module neighborhood information for BC5483

BC5483 has total of 24 gene neighbors in modules 126, 275
Gene neighbors (24)
Gene Common Name Description Module membership
BC0065 BC0065 Cell division protein DIVIC (NCBI ptt file) 41, 275
BC0066 BC0066 S1-type RNA-binding domain (NCBI ptt file) 275, 350
BC0292 BC0292 hypothetical protein (NCBI ptt file) 126, 300
BC1150 BC1150 IG hypothetical 15940 (NCBI ptt file) 126, 337
BC1291 BC1291 Transporter, MMPL family (NCBI ptt file) 126, 354
BC1382 BC1382 hypothetical protein (NCBI ptt file) 126, 180
BC1834 BC1834 Arsenical-resistance protein ACR3 (NCBI ptt file) 126, 296
BC2231 BC2231 hypothetical Cytosolic Protein (NCBI ptt file) 126, 296
BC3868 BC3868 DNA-directed RNA polymerase omega chain (NCBI ptt file) 275, 479
BC3871 BC3871 Protein yicC (NCBI ptt file) 142, 275
BC3917 BC3917 Cell division protein ftsL (NCBI ptt file) 228, 275
BC3953 BC3953 hypothetical protein (NCBI ptt file) 126, 296
BC4168 BC4168 hypothetical protein (NCBI ptt file) 126, 350
BC4333 BC4333 putative lipase (NCBI ptt file) 275, 426
BC4694 BC4694 hypothetical protein (NCBI ptt file) 275, 466
BC4796 BC4796 hypothetical Membrane Spanning Protein (NCBI ptt file) 64, 126
BC4991 BC4991 Glycine cleavage system H protein (NCBI ptt file) 74, 126
BC4992 BC4992 Arsenate reductase family protein (NCBI ptt file) 119, 126
BC5010 BC5010 Transcriptional regulator (NCBI ptt file) 126, 216
BC5052 BC5052 None 103, 126
BC5323 BC5323 hypothetical protein (NCBI ptt file) 126, 187
BC5376 BC5376 hypothetical Cytosolic Protein (NCBI ptt file) 117, 126
BC5396 BC5396 hydrolase (HAD superfamily) (NCBI ptt file) 103, 126
BC5483 BC5483 Stage 0 sporulation protein J (NCBI ptt file) 126, 275
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 BC5483
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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