Organism : Bacillus cereus ATCC14579 | Module List :
BC3645

CcdC protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Membrane protein involved in cytochrome C biogenesis cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3645
(Mouseover regulator name to see its description)

BC3645 is regulated by 27 influences and regulates 0 modules.
Regulators for BC3645 (27)
Regulator Module Operator
BC0649 63 tf
BC0758 63 tf
BC0950 63 tf
BC2444 63 tf
BC2794 63 tf
BC3160 63 tf
BC3244 63 tf
BC3493 63 tf
BC3497 63 tf
BC0047 285 tf
BC0059 285 tf
BC0116 285 tf
BC0657 285 tf
BC1075 285 tf
BC1077 285 tf
BC1113 285 tf
BC1387 285 tf
BC1710 285 tf
BC2362 285 tf
BC3493 285 tf
BC4029 285 tf
BC4356 285 tf
BC4525 285 tf
BC4581 285 tf
BC4834 285 tf
BC5340 285 tf
BC5373 285 tf

Warning: BC3645 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
4046 1.20e+04 GaGgaggA
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4047 1.90e+04 CAGCGCCc
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4486 2.90e+01 ccCC..cac.agCC
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4487 1.30e+03 AGGAgg
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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 BC3645

BC3645 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Membrane protein involved in cytochrome C biogenesis cog/ cog
Module neighborhood information for BC3645

BC3645 has total of 53 gene neighbors in modules 63, 285
Gene neighbors (53)
Gene Common Name Description Module membership
BC0013 BC0013 Inosine-5'-monophosphate dehydrogenase (NCBI ptt file) 63, 137
BC0046 BC0046 Dimethyladenosine transferase (NCBI ptt file) 285, 394
BC0048 BC0048 VEG protein (NCBI ptt file) 225, 285
BC0107 BC0107 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (NCBI ptt file) 285, 394
BC0545 BC0545 hypothetical Cytosolic Protein (NCBI ptt file) 285, 476
BC0565 BC0565 Ankyrin (NCBI ptt file) 63, 265
BC0572 BC0572 Two-component response regulator (NCBI ptt file) 63, 286
BC0649 BC0649 Transcriptional regulator, DeoR family (NCBI ptt file) 63, 246
BC0766 BC0766 Methylthioribose transport system permease protein (NCBI ptt file) 20, 63
BC1097 BC1097 hypothetical protein (NCBI ptt file) 63, 286
BC1166 BC1166 hypothetical Exported Protein (NCBI ptt file) 285, 400
BC1258 BC1258 hypothetical protein (NCBI ptt file) 63, 427
BC1774 BC1774 Peptide methionine sulfoxide reductase (NCBI ptt file) 63, 260
BC1840 BC1840 Transporter, Drug/Metabolite Exporter family (NCBI ptt file) 63, 141
BC1912 BC1912 Phage protein (NCBI ptt file) 63, 137
BC1913 BC1913 Phage protein (NCBI ptt file) 63, 137
BC1914 BC1914 Phage protein (NCBI ptt file) 63, 146
BC2315 BC2315 DinB protein (NCBI ptt file) 63, 163
BC2428 BC2428 hypothetical protein (NCBI ptt file) 63, 225
BC2539 BC2539 Two-component sensor kinase yxdK (NCBI ptt file) 6, 63
BC2540 BC2540 hypothetical protein (NCBI ptt file) 285, 430
BC2603 BC2603 hypothetical protein (NCBI ptt file) 63, 299
BC2740 BC2740 Protein translocase subunit SecY (NCBI ptt file) 6, 63
BC2794 BC2794 RNA polymerase ECF-type sigma factor (NCBI ptt file) 63, 105
BC3148 BC3148 Streptothricin acetyltransferase (NCBI ptt file) 63, 364
BC3407 BC3407 Cyclopropane-fatty-acyl-phospholipid synthase (NCBI ptt file) 228, 285
BC3497 BC3497 Transcriptional regulator, ArsR family (NCBI ptt file) 63, 146
BC3498 BC3498 Quinone oxidoreductase (NCBI ptt file) 63, 465
BC3584 BC3584 Oligopeptide-binding protein oppA (NCBI ptt file) 55, 63
BC3645 BC3645 CcdC protein (NCBI ptt file) 63, 285
BC3747 BC3747 Sensory box/GGDEF family protein (NCBI ptt file) 63, 286
BC3876 BC3876 hypothetical protein (NCBI ptt file) 63, 228
BC4014 BC4014 Neopullulanase (NCBI ptt file) 63, 299
BC4131 BC4131 hypothetical protein (NCBI ptt file) 63, 299
BC4146 BC4146 Protein erfK/srfK precursor (NCBI ptt file) 20, 63
BC4147 BC4147 Integral membrane protein (NCBI ptt file) 63, 482
BC4305 BC4305 hypothetical Cytosolic Protein (NCBI ptt file) 63, 72
BC4440 BC4440 Stage IV sporulation protein FB (NCBI ptt file) 252, 285
BC4464 BC4464 Folylpolyglutamate synthase (NCBI ptt file) 48, 63
BC4514 BC4514 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 63, 288
BC4568 BC4568 Multidrug resistance protein B (NCBI ptt file) 285, 394
BC4569 BC4569 Multidrug resistance protein A (NCBI ptt file) 179, 285
BC4666 BC4666 Two component system histidine kinase (NCBI ptt file) 63, 308
BC4671 BC4671 hypothetical protein (NCBI ptt file) 285, 430
BC4839 BC4839 ABC transporter ATP-binding protein (NCBI ptt file) 63, 453
BC4946 BC4946 hypothetical protein (NCBI ptt file) 63, 330
BC4947 BC4947 hypothetical protein (NCBI ptt file) 20, 63
BC4953 BC4953 hypothetical protein (NCBI ptt file) 285, 337
BC4965 BC4965 hypothetical Cytosolic Protein (NCBI ptt file) 281, 285
BC5067 BC5067 CrcB family protein (NCBI ptt file) 285, 394
BC5068 BC5068 CrcB family protein (NCBI ptt file) 63, 285
BC5328 BC5328 Methyltransferase (NCBI ptt file) 285, 430
BC5375 BC5375 Multimodular transpeptidase-transglycosylase PBP 2D (NCBI ptt file) 285, 311
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 BC3645
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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