Organism : Bacillus cereus ATCC14579 | Module List :
BC2752

hypothetical Membrane Spanning Protein (NCBI ptt file)

CircVis
Functional Annotations (5)
Function System
extracellular region go/ cellular_component
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
zinc ion binding go/ molecular_function
spore_YpeB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2752
(Mouseover regulator name to see its description)

BC2752 is regulated by 22 influences and regulates 0 modules.
Regulators for BC2752 (22)
Regulator Module Operator
BC0477 128 tf
BC1814 128 tf
BC2680 128 tf
BC2811 128 tf
BC3039 128 tf
BC3320 128 tf
BC3332 128 tf
BC3982 128 tf
BC4181 128 tf
BC5250 128 tf
BC0477 459 tf
BC0647 459 tf
BC0648 459 tf
BC1329 459 tf
BC2469 459 tf
BC2517 459 tf
BC2680 459 tf
BC2837 459 tf
BC2964 459 tf
BC3903 459 tf
BC5251 459 tf
BC5282 459 tf

Warning: BC2752 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
4172 1.60e-01 cCCTcC
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4173 8.40e+03 TTCcaTaCtAAaCAcccAcC
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4828 2.30e-02 AAAAg.GagGaa
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4829 1.00e+02 cCCtCc
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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 BC2752

BC2752 is enriched for 5 functions in 4 categories.
Enrichment Table (5)
Function System
extracellular region go/ cellular_component
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
zinc ion binding go/ molecular_function
spore_YpeB tigr/ tigrfam
Module neighborhood information for BC2752

BC2752 has total of 39 gene neighbors in modules 128, 459
Gene neighbors (39)
Gene Common Name Description Module membership
BC0212 BC0212 hypothetical protein (NCBI ptt file) 9, 128
BC0477 BC0477 Transcriptional regulator (NCBI ptt file) 272, 459
BC0891 BC0891 hypothetical protein (NCBI ptt file) 128, 415
BC0987 BC0987 hypothetical protein (NCBI ptt file) 128, 415
BC1084 BC1084 hypothetical protein (NCBI ptt file) 128, 284
BC1221 BC1221 hypothetical Membrane Spanning Protein (NCBI ptt file) 128, 185
BC1274 BC1274 hypothetical protein (NCBI ptt file) 25, 128
BC1280 BC1280 hypothetical protein (NCBI ptt file) 128, 138
BC1418 BC1418 hypothetical protein (NCBI ptt file) 128, 354
BC1429 BC1429 hypothetical protein (NCBI ptt file) 128, 334
BC1608 BC1608 hypothetical Membrane Spanning Protein (NCBI ptt file) 289, 459
BC1831 BC1831 hypothetical protein (NCBI ptt file) 128, 158
BC1942 BC1942 hypothetical protein (NCBI ptt file) 128, 131
BC2138 BC2138 hypothetical protein (NCBI ptt file) 128, 317
BC2285 BC2285 2-methylcitrate synthase (NCBI ptt file) 232, 459
BC2287 BC2287 Methylisocitrate lyase (NCBI ptt file) 355, 459
BC2316 BC2316 Thermitase (NCBI ptt file) 289, 459
BC2355 BC2355 hypothetical protein (NCBI ptt file) 128, 280
BC2572 BC2572 Phage protein (NCBI ptt file) 355, 459
BC2608 BC2608 hypothetical Cytosolic Protein (NCBI ptt file) 31, 459
BC2647 BC2647 hypothetical protein (NCBI ptt file) 186, 459
BC2678 BC2678 hypothetical protein (NCBI ptt file) 339, 459
BC2694 BC2694 hypothetical protein (NCBI ptt file) 128, 189
BC2751 BC2751 IG hypothetical 17041 (NCBI ptt file) 253, 459
BC2752 BC2752 hypothetical Membrane Spanning Protein (NCBI ptt file) 128, 459
BC2753 BC2753 Cell wall hydrolase cwlJ (NCBI ptt file) 334, 459
BC2754 BC2754 hypothetical protein (NCBI ptt file) 46, 459
BC2980 BC2980 Arginine permease (NCBI ptt file) 294, 459
BC3092 BC3092 Glutathione-dependent formaldehyde dehydrogenase (NCBI ptt file) 128, 131
BC3403 BC3403 hypothetical protein (NCBI ptt file) 131, 459
BC3444 BC3444 hypothetical protein (NCBI ptt file) 128, 498
BC3508 BC3508 hypothetical protein (NCBI ptt file) 128, 337
BC3752 BC3752 None 128, 303
BC4047 BC4047 hypothetical protein (NCBI ptt file) 128, 358
BC4185 BC4185 hypothetical protein (NCBI ptt file) 128, 317
BC4228 BC4228 hypothetical protein (NCBI ptt file) 25, 128
BC4409 BC4409 hypothetical protein (NCBI ptt file) 128, 272
BC4418 BC4418 hypothetical protein (NCBI ptt file) 128, 227
BC4635 BC4635 hypothetical protein (NCBI ptt file) 128, 334
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 BC2752
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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