Organism : Bacillus cereus ATCC14579 | Module List :
BC2879

hypothetical protein (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC2879
(Mouseover regulator name to see its description)

BC2879 is regulated by 26 influences and regulates 0 modules.
Regulators for BC2879 (26)
Regulator Module Operator
BC0082 227 tf
BC0122 227 tf
BC0405 227 tf
BC0880 227 tf
BC1695 227 tf
BC1703 227 tf
BC2738 227 tf
BC3062 227 tf
BC3244 227 tf
BC3813 227 tf
BC3814 227 tf
BC4703 227 tf
BC5481 227 tf
BC0742 90 tf
BC0880 90 tf
BC1282 90 tf
BC1363 90 tf
BC1603 90 tf
BC1818 90 tf
BC2218 90 tf
BC2517 90 tf
BC2971 90 tf
BC2988 90 tf
BC4240 90 tf
BC5339 90 tf
BC5481 90 tf

Warning: BC2879 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
4096 1.80e+02 cccCCTtT
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4097 2.30e+04 CcTGCaAATaCGCc
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4370 1.50e+02 gtaaAGGAG.ga.Aa
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4371 3.40e+03 gAGGTGaAgAa
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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 BC2879

Warning: No Functional annotations were found!

Module neighborhood information for BC2879

BC2879 has total of 42 gene neighbors in modules 90, 227
Gene neighbors (42)
Gene Common Name Description Module membership
BC0159 BC0159 LSU ribosomal protein L17P (NCBI ptt file) 90, 430
BC0457 BC0457 Tetratricopeptide repeat family protein (NCBI ptt file) 90, 296
BC0546 BC0546 23S rRNA methyltransferase (NCBI ptt file) 90, 380
BC0644 BC0644 OsmC-like protein (NCBI ptt file) 227, 473
BC0739 BC0739 hypothetical protein (NCBI ptt file) 90, 478
BC0740 BC0740 Cell wall endopeptidase, family M23/M37 (NCBI ptt file) 15, 90
BC1086 BC1086 Lipoate-protein ligase A (NCBI ptt file) 180, 227
BC1460 BC1460 hypothetical protein (NCBI ptt file) 227, 480
BC1515 BC1515 Nucleoside diphosphate kinase (NCBI ptt file) 187, 227
BC1598 BC1598 LACX protein (NCBI ptt file) 90, 296
BC1624 BC1624 hydrolase (HAD superfamily) (NCBI ptt file) 20, 227
BC1693 BC1693 putative hydrolase (NCBI ptt file) 227, 303
BC1694 BC1694 hypothetical protein (NCBI ptt file) 227, 333
BC1924 BC1924 L-lactate dehydrogenase (NCBI ptt file) 90, 100
BC2153 BC2153 hypothetical protein (NCBI ptt file) 28, 227
BC2210 BC2210 NAD(P)H nitroreductase (NCBI ptt file) 90, 406
BC2242 BC2242 hypothetical Cytosolic Protein (NCBI ptt file) 216, 227
BC2439 BC2439 Aminoacyl-histidine dipeptidase (NCBI ptt file) 180, 227
BC2671 BC2671 ThiJ/PfpI family (NCBI ptt file) 20, 90
BC2826 BC2826 Manganese-dependent inorganic pyrophosphatase (NCBI ptt file) 187, 227
BC2828 BC2828 Acetyltransferase (NCBI ptt file) 90, 426
BC2879 BC2879 hypothetical protein (NCBI ptt file) 90, 227
BC2987 BC2987 hypothetical Membrane Spanning Protein (NCBI ptt file) 90, 304
BC2989 BC2989 hypothetical protein (NCBI ptt file) 90, 304
BC3728 BC3728 DNA-binding protein HU (NCBI ptt file) 74, 227
BC4107 BC4107 hypothetical Cytosolic Protein (NCBI ptt file) 227, 304
BC4384 BC4384 hypothetical protein (NCBI ptt file) 28, 227
BC4418 BC4418 hypothetical protein (NCBI ptt file) 128, 227
BC4519 BC4519 hypothetical Cytosolic Protein (NCBI ptt file) 90, 304
BC4712 BC4712 hypothetical Cytosolic Protein (NCBI ptt file) 146, 227
BC4713 BC4713 hypothetical protein (NCBI ptt file) 227, 454
BC4728 BC4728 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 41, 90
BC4791 BC4791 Carbonic anhydrase (NCBI ptt file) 227, 480
BC4815 BC4815 Hypoxanthine-guanine phosphoribosyltransferase (NCBI ptt file) 90, 198
BC4861 BC4861 hypothetical protein (NCBI ptt file) 90, 380
BC4900 BC4900 S1-type RNA-binding domain (NCBI ptt file) 129, 227
BC4909 BC4909 Kinase-associated protein B (NCBI ptt file) 74, 227
BC4913 BC4913 hypothetical protein (NCBI ptt file) 15, 90
BC5220 BC5220 Lactoylglutathione lyase (NCBI ptt file) 90, 198
BC5380 BC5380 Ferrichrome-binding protein (NCBI ptt file) 90, 201
BC5388 BC5388 IG hypothetical 16794 (NCBI ptt file) 74, 227
BC5397 BC5397 hypothetical Membrane Spanning Protein (NCBI ptt file) 90, 170
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 BC2879
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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