Organism : Bacillus cereus ATCC14579 | Module List :
BC0547

Sensory box/GGDEF family protein (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain cog/ cog
signal transducer activity go/ molecular_function
signal transduction go/ biological_process
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0547
(Mouseover regulator name to see its description)

BC0547 is regulated by 33 influences and regulates 0 modules.
Regulators for BC0547 (33)
Regulator Module Operator
BC0785 34 tf
BC1032 34 tf
BC1080 34 tf
BC2410 34 tf
BC2672 34 tf
BC2738 34 tf
BC2760 34 tf
BC2770 34 tf
BC2801 34 tf
BC2988 34 tf
BC3244 34 tf
BC4072 34 tf
BC4104 34 tf
BC4499 34 tf
BC4661 34 tf
BC5205 34 tf
BC0213 238 tf
BC1032 238 tf
BC1080 238 tf
BC2362 238 tf
BC2526 238 tf
BC2551 238 tf
BC2670 238 tf
BC2738 238 tf
BC2801 238 tf
BC2811 238 tf
BC2936 238 tf
BC3449 238 tf
BC3493 238 tf
BC3589 238 tf
BC4316 238 tf
BC4374 238 tf
BC5205 238 tf

Warning: BC0547 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
3990 4.70e+02 taatcTCtttttttt
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3991 5.40e+03 aaGgagGA
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4392 2.50e+03 agGgGgTgta
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4393 1.50e+03 gAAaaGGAGG
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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 BC0547

BC0547 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain cog/ cog
signal transducer activity go/ molecular_function
signal transduction go/ biological_process
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
sensory_box tigr/ tigrfam
Module neighborhood information for BC0547

BC0547 has total of 41 gene neighbors in modules 34, 238
Gene neighbors (41)
Gene Common Name Description Module membership
BC0547 BC0547 Sensory box/GGDEF family protein (NCBI ptt file) 34, 238
BC0985 BC0985 hypothetical protein (NCBI ptt file) 85, 238
BC0989 BC0989 hypothetical protein (NCBI ptt file) 238, 241
BC1026 BC1026 Response regulator aspartate phosphatase (NCBI ptt file) 46, 238
BC1062 BC1062 3-oxoacyl-[acyl-carrier protein] reductase (NCBI ptt file) 34, 330
BC1261 BC1261 ATP/GTP-binding protein (NCBI ptt file) 238, 316
BC1262 BC1262 hypothetical protein (NCBI ptt file) 238, 316
BC1271 BC1271 hypothetical protein (NCBI ptt file) 238, 411
BC1466 BC1466 hypothetical protein (NCBI ptt file) 34, 488
BC1658 BC1658 Flagellin (NCBI ptt file) 52, 238
BC1799 BC1799 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 34, 137
BC2141 BC2141 Lipase (NCBI ptt file) 125, 238
BC2142 BC2142 Stage V sporulation protein S (NCBI ptt file) 34, 137
BC2143 BC2143 hypothetical Cytosolic Protein (NCBI ptt file) 34, 362
BC2144 BC2144 5-methylcytosine-specific restriction enzyme A (NCBI ptt file) 34, 154
BC2154 BC2154 Single-strand DNA binding protein (NCBI ptt file) 238, 255
BC2162 BC2162 Methyltransferase (NCBI ptt file) 25, 238
BC2314 BC2314 hypothetical protein (NCBI ptt file) 238, 316
BC2331 BC2331 Inosine-uridine preferring nucleoside hydrolase (NCBI ptt file) 154, 238
BC2349 BC2349 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 238, 525
BC2467 BC2467 D-alanyl-D-alanine carboxypeptidase (NCBI ptt file) 189, 238
BC2551 BC2551 Transcriptional activator tenA (NCBI ptt file) 25, 238
BC2553 BC2553 hypothetical protein (NCBI ptt file) 171, 238
BC2611 BC2611 Virginiamycin A acetyltransferase (NCBI ptt file) 56, 238
BC2730 BC2730 2-haloalkanoic acid dehalogenase (NCBI ptt file) 34, 525
BC2747 BC2747 hypothetical Cytosolic Protein (NCBI ptt file) 238, 454
BC2858 BC2858 hypothetical protein (NCBI ptt file) 125, 238
BC2906 BC2906 hypothetical protein (NCBI ptt file) 25, 238
BC2927 BC2927 Prolyl endopeptidase (NCBI ptt file) 158, 238
BC3158 BC3158 Pyrimidine Reductase (NCBI ptt file) 34, 212
BC3262 BC3262 hypothetical protein (NCBI ptt file) 34, 238
BC3465 BC3465 Acetyltransferase (NCBI ptt file) 34, 336
BC3533 BC3533 Vancomycin B-type resistance protein vanW (NCBI ptt file) 34, 377
BC4006 BC4006 hypothetical Cytosolic Protein (NCBI ptt file) 123, 238
BC4134 BC4134 Pyrroline-5-carboxylate reductase (NCBI ptt file) 34, 377
BC4244 BC4244 hypothetical protein (NCBI ptt file) 34, 160
BC4255 BC4255 Isochorismatase (NCBI ptt file) 72, 238
BC4374 BC4374 Transcription elongation factor greA (NCBI ptt file) 238, 241
BC4665 BC4665 Two-component response regulator (NCBI ptt file) 238, 316
BC4905 BC4905 hypothetical protein (NCBI ptt file) 238, 308
BC5116 BC5116 hypothetical protein (NCBI ptt file) 34, 248
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 BC0547
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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