Organism : Bacillus cereus ATCC14579 | Module List :
BC4395

Prespore specific transcriptional activator rsfA (NCBI ptt file)

CircVis
Functional Annotations (2)
Function System
nucleus go/ cellular_component
DNA_bind_RsfA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4395
(Mouseover regulator name to see its description)

BC4395 is regulated by 28 influences and regulates 5 modules.
Regulators for BC4395 (28)
Regulator Module Operator
BC1490 343 tf
BC1889 343 tf
BC2178 343 tf
BC2367 343 tf
BC2401 343 tf
BC2517 343 tf
BC2903 343 tf
BC2988 343 tf
BC3160 343 tf
BC3194 343 tf
BC3704 343 tf
BC4395 343 tf
BC4611 343 tf
BC5251 343 tf
BC5340 343 tf
BC0213 122 tf
BC0586 122 tf
BC1302 122 tf
BC2631 122 tf
BC3025 122 tf
BC3400 122 tf
BC3976 122 tf
BC4181 122 tf
BC4211 122 tf
BC4277 122 tf
BC4395 122 tf
BC4474 122 tf
BC4570 122 tf

Warning: BC4395 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
4160 1.60e+02 gccCaattCaC
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4161 1.10e+03 AaaGGaGa
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4598 9.50e-03 aAAGGAGg
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4599 9.00e+03 GGGCAGc
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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 BC4395

BC4395 is enriched for 2 functions in 4 categories.
Enrichment Table (2)
Function System
nucleus go/ cellular_component
DNA_bind_RsfA tigr/ tigrfam
Module neighborhood information for BC4395

BC4395 has total of 36 gene neighbors in modules 122, 343
Gene neighbors (36)
Gene Common Name Description Module membership
BC0193 BC0193 hypothetical protein (NCBI ptt file) 343, 440
BC0381 BC0381 Ferrichrome transport system permease protein fhuG (NCBI ptt file) 122, 467
BC0382 BC0382 Ferrichrome transport system permease protein fhuB (NCBI ptt file) 122, 467
BC0383 BC0383 Ferrichrome-binding protein (NCBI ptt file) 122, 467
BC0941 BC0941 Type II restriction-modification system methylation subunit (NCBI ptt file) 257, 343
BC0995 BC0995 hypothetical protein (NCBI ptt file) 343, 443
BC1022 BC1022 hypothetical protein (NCBI ptt file) 122, 507
BC1495 BC1495 Thioredoxin reductase (NCBI ptt file) 122, 262
BC1556 BC1556 hypothetical protein (NCBI ptt file) 263, 343
BC1557 BC1557 hypothetical protein (NCBI ptt file) 122, 262
BC1953 BC1953 Enterotoxin (NCBI ptt file) 343, 442
BC2067 BC2067 hypothetical Membrane Spanning Protein (NCBI ptt file) 343, 503
BC2695 BC2695 Outer membrane protein romA (NCBI ptt file) 170, 343
BC2698 BC2698 hypothetical Cytosolic Protein (NCBI ptt file) 15, 343
BC2894 BC2894 Macrolide-efflux protein (NCBI ptt file) 257, 343
BC3209 BC3209 hypothetical Cytosolic Protein (NCBI ptt file) 343, 465
BC3344 BC3344 Ribosomal-protein-alanine acetyltransferase (NCBI ptt file) 343, 414
BC3396 BC3396 hypothetical Membrane Spanning Protein (NCBI ptt file) 18, 122
BC3958 BC3958 Myo-inositol-1(or 4)-monophosphatase (NCBI ptt file) 122, 527
BC4123 BC4123 Lipase/Acylhydrolase with GDSL-like motif (NCBI ptt file) 20, 343
BC4394 BC4394 ATPase, AAA family (NCBI ptt file) 122, 394
BC4395 BC4395 Prespore specific transcriptional activator rsfA (NCBI ptt file) 122, 343
BC4400 BC4400 D-tyrosyl-tRNA(Tyr) deacylase (NCBI ptt file) 122, 262
BC4401 BC4401 GTP pyrophosphokinase (NCBI ptt file) 71, 122
BC4408 BC4408 hypothetical Membrane Associated Protein (NCBI ptt file) 343, 354
BC4468 BC4468 Glutamate-1-semialdehyde 2,1-aminomutase (NCBI ptt file) 51, 122
BC4469 BC4469 Delta-aminolevulinic acid dehydratase (NCBI ptt file) 51, 122
BC4470 BC4470 Uroporphyrinogen-III synthase (NCBI ptt file) 51, 122
BC4471 BC4471 Porphobilinogen deaminase (NCBI ptt file) 51, 122
BC4472 BC4472 HEMX protein (NCBI ptt file) 51, 122
BC4473 BC4473 Glutamyl-tRNA reductase (NCBI ptt file) 51, 122
BC4496 BC4496 Glutamate racemase (NCBI ptt file) 122, 302
BC4752 BC4752 hypothetical protein (NCBI ptt file) 122, 439
BC4957 BC4957 hypothetical protein (NCBI ptt file) 343, 443
BC4994 BC4994 Ser/Thr and Tyr protein phosphatase (dual specificity) (NCBI ptt file) 18, 122
BC5382 BC5382 Ferrichrome transport system permease protein fhuG (NCBI ptt file) 122, 467
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 BC4395
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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