Organism : Bacillus cereus ATCC14579 | Module List :
BC1842

RRF2 family protein (NCBI ptt file)

CircVis
Functional Annotations (1)
Function System
Predicted transcriptional regulator cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC1842
(Mouseover regulator name to see its description)

BC1842 is regulated by 10 influences and regulates 7 modules.
Regulators for BC1842 (10)
Regulator Module Operator
BC0566 368 tf
BC0840 368 tf
BC0848 368 tf
BC1842 368 tf
BC3155 368 tf
BC1037 33 tf
BC1842 33 tf
BC2773 33 tf
BC3155 33 tf
BC4474 33 tf

Warning: BC1842 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
3988 6.30e+01 ACTTcCatAaagtAAgTtAatgc
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3989 2.70e+01 tCatcATAAAatTTttTtg
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4646 2.30e+00 TGtAAcTataATgATTAcaac
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4647 2.30e+03 gGgGGAaG
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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 BC1842

BC1842 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted transcriptional regulator cog/ cog
Module neighborhood information for BC1842

BC1842 has total of 35 gene neighbors in modules 33, 368
Gene neighbors (35)
Gene Common Name Description Module membership
BC0793 BC0793 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 33, 305
BC0845 BC0845 hypothetical protein (NCBI ptt file) 91, 368
BC0846 BC0846 hypothetical protein (NCBI ptt file) 91, 368
BC0856 BC0856 Transcriptional regulator, MarR family (NCBI ptt file) 33, 76
BC0857 BC0857 hypothetical protein (NCBI ptt file) 33, 305
BC0858 BC0858 Modulator of drug activity B (NCBI ptt file) 33, 305
BC0912 BC0912 Thioredoxin (NCBI ptt file) 91, 368
BC0913 BC0913 hypothetical Cytosolic Protein (NCBI ptt file) 91, 368
BC0914 BC0914 hypothetical protein (NCBI ptt file) 91, 368
BC0915 BC0915 hypothetical protein (NCBI ptt file) 91, 368
BC1027 BC1027 Lipase (NCBI ptt file) 91, 368
BC1029 BC1029 IG hypothetical 18063 (NCBI ptt file) 33, 281
BC1364 BC1364 hypothetical protein (NCBI ptt file) 33, 281
BC1835 BC1835 FMN-dependent NADH-azoreductase (NCBI ptt file) 33, 305
BC1838 BC1838 Copper resistance protein (NCBI ptt file) 33, 368
BC1839 BC1839 hypothetical Membrane Associated Protein (NCBI ptt file) 33, 368
BC1842 BC1842 RRF2 family protein (NCBI ptt file) 33, 368
BC1843 BC1843 2-hydroxychromene-2-carboxylate isomerase family protein (NCBI ptt file) 91, 368
BC1844 BC1844 Nitroreductase family protein (NCBI ptt file) 91, 368
BC2772 BC2772 Methyltransferase (NCBI ptt file) 33, 305
BC3152 BC3152 Arsenate reductase (NCBI ptt file) 33, 305
BC3153 BC3153 Arsenical-resistance protein ACR3 (NCBI ptt file) 33, 305
BC3154 BC3154 Lactoylglutathione lyase (NCBI ptt file) 33, 305
BC3155 BC3155 Arsenical resistance operon repressor (NCBI ptt file) 33, 368
BC3321 BC3321 NAD(P)H-dependent flavin reductase (NCBI ptt file) 33, 305
BC3386 BC3386 hydrolase (HAD superfamily) (NCBI ptt file) 33, 368
BC3387 BC3387 Diaminohydroxyphosphoribosylaminopyrimidine deaminase (NCBI ptt file) 33, 368
BC3388 BC3388 GTP cyclohydrolase II (NCBI ptt file) 33, 368
BC3412 BC3412 Microbial collagenase (NCBI ptt file) 33, 368
BC3642 BC3642 Carboxylesterase (NCBI ptt file) 33, 505
BC3643 BC3643 Glyoxalase family protein (NCBI ptt file) 33, 305
BC4474 BC4474 Transcriptional regulator, MarR family (NCBI ptt file) 33, 305
BC4475 BC4475 Osmotically inducible protein C (NCBI ptt file) 33, 305
BC5054 BC5054 putative NAD-dependent dehydrogenase (NCBI ptt file) 91, 368
BC5321 BC5321 hypothetical Membrane Spanning Protein (NCBI ptt file) 33, 305
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 BC1842
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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