Organism : Bacillus cereus ATCC14579 | Module List :
BC2495

hypothetical protein (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2495
(Mouseover regulator name to see its description)

BC2495 is regulated by 26 influences and regulates 0 modules.
Regulators for BC2495 (26)
Regulator Module Operator
BC0213 141 tf
BC0690 141 tf
BC1731 141 tf
BC2526 141 tf
BC3175 141 tf
BC3593 141 tf
BC4181 141 tf
BC4314 141 tf
BC4703 141 tf
BC5175 141 tf
BC5222 141 tf
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

Warning: BC2495 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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4198 5.30e-09 aa.aAagGaG.ta
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4199 2.40e+04 ATgTTTGG.AGgGG
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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 BC2495

Warning: No Functional annotations were found!

Module neighborhood information for BC2495

BC2495 has total of 86 gene neighbors in modules 85, 141
Gene neighbors (86)
Gene Common Name Description Module membership
BC0172 BC0172 hypothetical protein (NCBI ptt file) 141, 158
BC0222 BC0222 Periplasmic molybdate-binding protein (NCBI ptt file) 85, 395
BC0358 BC0358 Quaternary ammonium compound-resistance protein (NCBI ptt file) 72, 85
BC0399 BC0399 Oxidoreductase (NCBI ptt file) 30, 85
BC0494 BC0494 hypothetical Cytosolic Protein (NCBI ptt file) 85, 139
BC0563 BC0563 Biotin carboxyl carrier protein (NCBI ptt file) 9, 85
BC0675 BC0675 hypothetical protein (NCBI ptt file) 85, 138
BC0690 BC0690 Transcriptional regulator, PBSX family (NCBI ptt file) 141, 485
BC0771 BC0771 Protein erfK/srfK precursor (NCBI ptt file) 9, 85
BC0826 BC0826 hypothetical DNA-binding protein (NCBI ptt file) 141, 257
BC0827 BC0827 hypothetical protein (NCBI ptt file) 141, 218
BC0828 BC0828 Alkaline phosphatase like protein (NCBI ptt file) 141, 245
BC0831 BC0831 hypothetical protein (NCBI ptt file) 141, 487
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
BC0933 BC0933 hypothetical protein (NCBI ptt file) 141, 175
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
BC0997 BC0997 hypothetical protein (NCBI ptt file) 141, 358
BC1073 BC1073 hypothetical protein (NCBI ptt file) 85, 163
BC1109 BC1109 hypothetical protein (NCBI ptt file) 85, 404
BC1132 BC1132 hypothetical protein (NCBI ptt file) 141, 263
BC1281 BC1281 Cell envelope-bound metalloprotease (camelysin) (NCBI ptt file) 141, 293
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
BC1672 BC1672 Metal-dependent hydrolase related to alanyl-tRNA synthetase (NCBI ptt file) 141, 329
BC1677 BC1677 Dienelactone hydrolase family (NCBI ptt file) 141, 428
BC1691 BC1691 Phosphoglycerate mutase (NCBI ptt file) 25, 141
BC1840 BC1840 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 63, 141
BC1848 BC1848 Prophage helix-turn-helix protein (NCBI ptt file) 9, 85
BC1893 BC1893 Scaffold protein (NCBI ptt file) 141, 468
BC1935 BC1935 hypothetical protein (NCBI ptt file) 9, 85
BC2253 BC2253 hypothetical Cytosolic Protein (NCBI ptt file) 85, 154
BC2296 BC2296 Exonuclease SbcC (NCBI ptt file) 141, 193
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
BC2593 BC2593 Phage protein (NCBI ptt file) 25, 141
BC2620 BC2620 Penicillin-binding protein transpeptidase (NCBI ptt file) 9, 141
BC2622 BC2622 Macrolide glycosyltransferase (NCBI ptt file) 85, 250
BC2692 BC2692 Phosphohydrolase (MutT/nudix family protein) (NCBI ptt file) 141, 405
BC2819 BC2819 hypothetical protein (NCBI ptt file) 85, 489
BC2821 BC2821 Transposase (NCBI ptt file) 141, 245
BC2922 BC2922 hypothetical protein (NCBI ptt file) 141, 361
BC2961 BC2961 Sugar transport system permease protein (NCBI ptt file) 85, 158
BC3089 BC3089 Integral membrane protein (NCBI ptt file) 141, 396
BC3097 BC3097 Spore germination protein QC (NCBI ptt file) 24, 85
BC3105 BC3105 Transcriptional regulator, AraC family (NCBI ptt file) 9, 141
BC3138 BC3138 hypothetical protein (NCBI ptt file) 85, 364
BC3232 BC3232 hypothetical protein (NCBI ptt file) 85, 364
BC3238 BC3238 hypothetical protein (NCBI ptt file) 85, 364
BC3277 BC3277 hypothetical Cytosolic Protein (NCBI ptt file) 60, 141
BC3434 BC3434 Transcriptional regulator, DeoR family (NCBI ptt file) 9, 85
BC3594 BC3594 PhnB protein (NCBI ptt file) 141, 218
BC3689 BC3689 Site-specific recombinase (NCBI ptt file) 85, 415
BC3690 BC3690 LexA repressor (NCBI ptt file) 141, 158
BC3703 BC3703 Phage protein (NCBI ptt file) 9, 141
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
BC4120 BC4120 hypothetical protein (NCBI ptt file) 141, 184
BC4428 BC4428 ABC transporter permease protein (NCBI ptt file) 108, 141
BC4451 BC4451 hypothetical protein (NCBI ptt file) 141, 464
BC4612 BC4612 hypothetical protein (NCBI ptt file) 76, 141
BC4617 BC4617 hypothetical Membrane Spanning Protein (NCBI ptt file) 9, 141
BC4759 BC4759 hypothetical Membrane Spanning Protein (NCBI ptt file) 141, 281
BC4780 BC4780 ABC transporter permease protein (NCBI ptt file) 141, 199
BC4825 BC4825 ABC transporter ATP-binding protein (NCBI ptt file) 141, 385
BC4945 BC4945 None 9, 85
BC5254 BC5254 ABC transporter ATP-binding protein (NCBI ptt file) 141, 327
BC5303 BC5303 Integral membrane protein (NCBI ptt file) 141, 327
BC5346 BC5346 Cardiolipin synthetase (NCBI ptt file) 141, 456
BC5348 BC5348 None 141, 410
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 BC2495
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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