Organism : Bacillus cereus ATCC14579 | Module List :
BC0410

Transcription regulator, Crp family (NCBI ptt file)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC0410
(Mouseover regulator name to see its description)

BC0410 is regulated by 20 influences and regulates 13 modules.
Regulators for BC0410 (20)
Regulator Module Operator
BC0410 429 tf
BC0473 429 tf
BC0586 429 tf
BC1302 429 tf
BC1329 429 tf
BC2133 429 tf
BC2811 429 tf
BC3072 429 tf
BC4240 429 tf
BC4650 429 tf
BC5141 429 tf
BC0410 167 tf
BC1302 167 tf
BC1329 167 tf
BC2133 167 tf
BC3072 167 tf
BC3160 167 tf
BC4240 167 tf
BC4650 167 tf
BC5141 167 tf

Warning: BC0410 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
4250 1.10e-20 TTgt.aAaaatTTCACAaa
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4251 1.50e+00 AacAaaa.Agaaggg
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4768 5.70e-14 TTgt.aaaaatTTCAcAaa.aat
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4769 3.50e+02 AaatAc.AAagGag
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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 BC0410

BC0410 is enriched for 4 functions in 3 categories.
Module neighborhood information for BC0410

BC0410 has total of 27 gene neighbors in modules 167, 429
Gene neighbors (27)
Gene Common Name Description Module membership
BC0194 BC0194 hypothetical Membrane Spanning Protein (NCBI ptt file) 167, 429
BC0410 BC0410 Transcription regulator, Crp family (NCBI ptt file) 167, 429
BC0448 BC0448 Calcium-transporting ATPase (NCBI ptt file) 167, 190
BC0491 BC0491 Formate acetyltransferase (NCBI ptt file) 167, 429
BC0492 BC0492 Pyruvate formate-lyase activating enzyme (NCBI ptt file) 167, 190
BC0612 BC0612 L-lactate permease (NCBI ptt file) 167, 429
BC1308 BC1308 Nitrite transporter (NCBI ptt file) 167, 429
BC1688 BC1688 IG hypothetical 17894 (NCBI ptt file) 167, 429
BC1938 BC1938 Cytochrome d ubiquinol oxidase subunit I (NCBI ptt file) 429, 481
BC1939 BC1939 Cytochrome d ubiquinol oxidase subunit II (NCBI ptt file) 167, 429
BC1940 BC1940 Transport ATP-binding protein cydD (NCBI ptt file) 167, 429
BC1941 BC1941 Transport ATP-binding protein cydC (NCBI ptt file) 429, 481
BC2123 BC2123 Molybdenum cofactor biosynthesis protein A (NCBI ptt file) 167, 429
BC2124 BC2124 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 167, 429
BC2127 BC2127 Molybdopterin (MPT) converting factor, subunit 1 (NCBI ptt file) 190, 429
BC2220 BC2220 Alcohol dehydrogenase (NCBI ptt file) 167, 429
BC3603 BC3603 Anaerobic ribonucleoside-triphosphate reductase (NCBI ptt file) 167, 429
BC4025 BC4025 hypothetical protein (NCBI ptt file) 167, 454
BC4240 BC4240 Transcriptional regulator (NCBI ptt file) 167, 429
BC4364 BC4364 hypothetical Membrane Spanning Protein (NCBI ptt file) 167, 429
BC4365 BC4365 Alcohol dehydrogenase (NCBI ptt file) 167, 429
BC4792 BC4792 Cytochrome d ubiquinol oxidase subunit I (NCBI ptt file) 167, 429
BC4793 BC4793 Cytochrome d ubiquinol oxidase subunit II (NCBI ptt file) 167, 429
BC4870 BC4870 L-lactate dehydrogenase (NCBI ptt file) 167, 477
BC4995 BC4995 regulatory protein (pfoS/R) (NCBI ptt file) 167, 429
BC4996 BC4996 L-lactate dehydrogenase (NCBI ptt file) 167, 429
BC5219 BC5219 Integral membrane protein (NCBI ptt file) 167, 429
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 BC0410
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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