Organism : Bacillus cereus ATCC14579 | Module List :
BC3733

hypothetical protein (NCBI ptt file)

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC3733
(Mouseover regulator name to see its description)

BC3733 is regulated by 16 influences and regulates 0 modules.
Regulators for BC3733 (16)
Regulator Module Operator
BC1851 334 tf
BC2680 334 tf
BC2837 334 tf
BC2964 334 tf
BC3653 334 tf
BC0566 339 tf
BC1851 339 tf
BC2410 339 tf
BC2517 339 tf
BC2680 339 tf
BC2811 339 tf
BC2837 339 tf
BC2964 339 tf
BC3588 339 tf
BC3589 339 tf
BC3903 339 tf

Warning: BC3733 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
4580 1.70e-04 T.CCcCctTcattaT
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4581 6.70e+02 aaaGGaGG
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4590 5.60e-06 aaAGGgGG
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4591 5.00e+03 GGAGGGA
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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 BC3733

Warning: No Functional annotations were found!

Module neighborhood information for BC3733

BC3733 has total of 52 gene neighbors in modules 334, 339
Gene neighbors (52)
Gene Common Name Description Module membership
BC0309 BC0309 Methyltransferase (NCBI ptt file) 272, 339
BC0401 BC0401 Cystine transport system permease protein (NCBI ptt file) 289, 339
BC0635 BC0635 Spore germination protein KA (NCBI ptt file) 115, 339
BC0638 BC0638 Sodium/proton-dependent alanine carrier protein (NCBI ptt file) 339, 407
BC0641 BC0641 Glutamine transport system permease protein glnP (NCBI ptt file) 339, 340
BC0642 BC0642 Glutamine transport system permease protein glnP (NCBI ptt file) 339, 340
BC0823 BC0823 CotJA protein (NCBI ptt file) 26, 334
BC0878 BC0878 IG hypothetical 16724 (NCBI ptt file) 17, 334
BC0904 BC0904 hypothetical protein (NCBI ptt file) 17, 334
BC1078 BC1078 Phage infection protein (NCBI ptt file) 54, 339
BC1429 BC1429 hypothetical protein (NCBI ptt file) 128, 334
BC1573 BC1573 hypothetical protein (NCBI ptt file) 186, 334
BC1805 BC1805 hypothetical protein (NCBI ptt file) 186, 334
BC1808 BC1808 hypothetical protein (NCBI ptt file) 186, 334
BC1894 BC1894 Phage protein (NCBI ptt file) 272, 334
BC1905 BC1905 Phage protein (NCBI ptt file) 232, 334
BC1911 BC1911 N-acetylmuramoyl-L-alanine amidase (NCBI ptt file) 205, 334
BC1928 BC1928 Branched-chain amino acid transport ATP-binding protein livG (NCBI ptt file) 334, 520
BC2007 BC2007 hypothetical protein (NCBI ptt file) 186, 334
BC2010 BC2010 hypothetical Membrane Spanning Protein (NCBI ptt file) 334, 463
BC2091 BC2091 hypothetical protein (NCBI ptt file) 186, 334
BC2149 BC2149 hypothetical protein (NCBI ptt file) 334, 417
BC2222 BC2222 Oligopeptide transport system permease protein oppB (NCBI ptt file) 253, 339
BC2383 BC2383 Oxalate decarboxylase (NCBI ptt file) 272, 334
BC2509 BC2509 Sortase (NCBI ptt file) 17, 334
BC2651 BC2651 hypothetical protein (NCBI ptt file) 291, 339
BC2678 BC2678 hypothetical protein (NCBI ptt file) 339, 459
BC2712 BC2712 hypothetical protein (NCBI ptt file) 186, 334
BC2753 BC2753 Cell wall hydrolase cwlJ (NCBI ptt file) 334, 459
BC2875 BC2875 hypothetical protein (NCBI ptt file) 334, 339
BC2962 BC2962 Sugar transport system permease protein (NCBI ptt file) 199, 334
BC2972 BC2972 hypothetical protein (NCBI ptt file) 339, 397
BC2981 BC2981 hypothetical protein (NCBI ptt file) 146, 334
BC3357 BC3357 hypothetical protein (NCBI ptt file) 186, 339
BC3360 BC3360 Methyltransferase (NCBI ptt file) 17, 334
BC3397 BC3397 hypothetical protein (NCBI ptt file) 186, 334
BC3516 BC3516 CDP-abequose synthase (NCBI ptt file) 162, 339
BC3598 BC3598 hypothetical protein (NCBI ptt file) 186, 334
BC3733 BC3733 hypothetical protein (NCBI ptt file) 334, 339
BC3751 BC3751 hypothetical protein (NCBI ptt file) 334, 339
BC3928 BC3928 hypothetical Membrane Spanning Protein (NCBI ptt file) 131, 339
BC4002 BC4002 hypothetical protein (NCBI ptt file) 225, 334
BC4070 BC4070 Stage V sporulation protein AA (NCBI ptt file) 131, 334
BC4171 BC4171 hypothetical protein (NCBI ptt file) 17, 334
BC4407 BC4407 Stage V sporulation protein B (NCBI ptt file) 17, 339
BC4591 BC4591 MaoC family protein (NCBI ptt file) 199, 334
BC4595 BC4595 hypothetical protein (NCBI ptt file) 186, 334
BC4607 BC4607 hypothetical protein (NCBI ptt file) 217, 339
BC4635 BC4635 hypothetical protein (NCBI ptt file) 128, 334
BC4960 BC4960 Transcriptional regulator, DeoR family (NCBI ptt file) 30, 334
BC5134 BC5134 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 186, 334
BC5217 BC5217 PTS system, lichenan oligosaccharide-specific IIB component (NCBI ptt file) 199, 339
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 BC3733
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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