Organism : Bacillus cereus ATCC14579 | Module List :
BC3943

Cytochrome c oxidase polypeptide I (NCBI ptt file)

CircVis
Functional Annotations (14)
Function System
Heme/copper-type cytochrome/quinol oxidases, subunit 1 cog/ cog
cytochrome-c oxidase activity go/ molecular_function
iron ion binding go/ molecular_function
electron transport go/ biological_process
aerobic respiration go/ biological_process
aa3-type cytochrome c oxidase go/ molecular_function
ba3-type cytochrome c oxidase go/ molecular_function
caa3-type cytochrome c oxidase go/ molecular_function
cbb3-type cytochrome c oxidase go/ molecular_function
integral to membrane go/ cellular_component
heme binding go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
CtaD_CoxA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3943
(Mouseover regulator name to see its description)

BC3943 is regulated by 26 influences and regulates 0 modules.
Regulators for BC3943 (26)
Regulator Module Operator
BC0059 161 tf
BC0082 161 tf
BC0122 161 tf
BC0499 161 tf
BC0518 161 tf
BC0595 161 tf
BC0758 161 tf
BC1841 161 tf
BC2837 161 tf
BC3244 161 tf
BC3356 161 tf
BC3706 161 tf
BC3891 161 tf
BC3982 161 tf
BC4072 161 tf
BC4076 161 tf
BC5256 161 tf
BC0051 357 tf
BC0122 357 tf
BC0123 357 tf
BC0518 357 tf
BC1059 357 tf
BC1710 357 tf
BC2340 357 tf
BC4072 357 tf
BC4703 357 tf

Warning: BC3943 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
4238 4.10e+01 AggaAgG.GT
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4239 4.70e+03 AgAAaAAG
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4624 2.20e-01 AGatgctaggG
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4625 5.40e+02 AaGgGgtGcttgTTT
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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 BC3943

BC3943 is enriched for 14 functions in 3 categories.
Enrichment Table (14)
Function System
Heme/copper-type cytochrome/quinol oxidases, subunit 1 cog/ cog
cytochrome-c oxidase activity go/ molecular_function
iron ion binding go/ molecular_function
electron transport go/ biological_process
aerobic respiration go/ biological_process
aa3-type cytochrome c oxidase go/ molecular_function
ba3-type cytochrome c oxidase go/ molecular_function
caa3-type cytochrome c oxidase go/ molecular_function
cbb3-type cytochrome c oxidase go/ molecular_function
integral to membrane go/ cellular_component
heme binding go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
CtaD_CoxA tigr/ tigrfam
Module neighborhood information for BC3943

BC3943 has total of 39 gene neighbors in modules 161, 357
Gene neighbors (39)
Gene Common Name Description Module membership
BC0006 BC0006 DNA gyrase subunit A (NCBI ptt file) 75, 357
BC0109 BC0109 Serine acetyltransferase (NCBI ptt file) 240, 357
BC0110 BC0110 Cysteinyl-tRNA synthetase (NCBI ptt file) 240, 357
BC0111 BC0111 hypothetical protein (NCBI ptt file) 240, 357
BC0112 BC0112 23S rRNA methyltransferase (NCBI ptt file) 240, 357
BC0113 BC0113 hypothetical Cytosolic Protein (NCBI ptt file) 357, 484
BC0122 BC0122 DNA-directed RNA polymerase beta chain (NCBI ptt file) 357, 366
BC0123 BC0123 DNA-directed RNA polymerase beta' chain (NCBI ptt file) 357, 366
BC0339 BC0339 Geranylgeranylglyceryl diphosphate synthase (NCBI ptt file) 161, 319
BC0469 BC0469 None 161, 455
BC0855 BC0855 Multidrug resistance protein B (NCBI ptt file) 67, 161
BC1474 BC1474 ResB protein (NCBI ptt file) 150, 357
BC1475 BC1475 ResB protein (NCBI ptt file) 150, 357
BC1476 BC1476 Protein resC (NCBI ptt file) 150, 357
BC1499 BC1499 Isopentenyl-diphosphate delta-isomerase (NCBI ptt file) 27, 161
BC1729 BC1729 Multi-TM2 domain protein (NCBI ptt file) 161, 485
BC1730 BC1730 hypothetical protein (NCBI ptt file) 161, 485
BC2880 BC2880 Multidrug resistance protein B (NCBI ptt file) 161, 481
BC2881 BC2881 hypothetical Cytosolic Protein (NCBI ptt file) 161, 369
BC2984 BC2984 Immune inhibitor A precursor (NCBI ptt file) 357, 509
BC3094 BC3094 L-asparaginase (NCBI ptt file) 161, 399
BC3644 BC3644 Sodium/proline symporter (NCBI ptt file) 161, 388
BC3941 BC3941 Cytochrome c oxidase polypeptide IVB (NCBI ptt file) 357, 405
BC3942 BC3942 Cytochrome c oxidase polypeptide III (NCBI ptt file) 357, 405
BC3943 BC3943 Cytochrome c oxidase polypeptide I (NCBI ptt file) 161, 357
BC3944 BC3944 Cytochrome c oxidase polypeptide II (NCBI ptt file) 161, 357
BC3945 BC3945 Protoheme IX farnesyltransferase (NCBI ptt file) 161, 346
BC4173 BC4173 None 161, 265
BC4286 BC4286 NIF3-related protein (NCBI ptt file) 161, 192
BC4287 BC4287 hypothetical Cytosolic Protein (NCBI ptt file) 161, 192
BC4322 BC4322 ComE operon protein 3 (NCBI ptt file) 161, 346
BC4492 BC4492 putative phosphoesterase (NCBI ptt file) 182, 357
BC4494 BC4494 Ribonuclease PH (NCBI ptt file) 313, 357
BC5304 BC5304 None 161, 337
BC5305 BC5305 ATP synthase epsilon chain (NCBI ptt file) 182, 357
BC5306 BC5306 ATP synthase beta chain (NCBI ptt file) 182, 357
BC5307 BC5307 ATP synthase gamma chain (NCBI ptt file) 182, 357
BC5308 BC5308 F0F1 ATP synthase subunit alpha (RefSeq) 182, 357
BC5489 BC5489 Ribonuclease P protein component (NCBI ptt file) 142, 161
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 BC3943
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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