Organism : Bacillus cereus ATCC14579 | Module List :
BC4262

5-formyltetrahydrofolate cyclo-ligase (NCBI ptt file)

CircVis
Functional Annotations (7)
Function System
5-formyltetrahydrofolate cyclo-ligase cog/ cog
ATP binding go/ molecular_function
folic acid-containing compound biosynthetic process go/ biological_process
5-formyltetrahydrofolate cyclo-ligase activity go/ molecular_function
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
MTHFS_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for BC4262
(Mouseover regulator name to see its description)

BC4262 is regulated by 29 influences and regulates 0 modules.
Regulators for BC4262 (29)
Regulator Module Operator
BC0840 41 tf
BC1329 41 tf
BC1710 41 tf
BC1715 41 tf
BC1719 41 tf
BC2178 41 tf
BC2815 41 tf
BC3668 41 tf
BC3976 41 tf
BC4505 41 tf
BC4589 41 tf
BC4930 41 tf
BC5010 41 tf
BC5352 41 tf
BC0057 394 tf
BC1113 394 tf
BC1614 394 tf
BC1698 394 tf
BC1719 394 tf
BC2178 394 tf
BC2401 394 tf
BC3332 394 tf
BC3588 394 tf
BC3814 394 tf
BC3982 394 tf
BC4001 394 tf
BC4029 394 tf
BC4356 394 tf
BC5373 394 tf

Warning: BC4262 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
4002 2.50e-02 tttcccTTTct
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4003 2.10e+03 cCcGGGGC
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4698 3.40e+01 aGGAGG
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4699 5.50e+03 CGgcAaaAacg.GgcgtTtc
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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 BC4262

BC4262 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
5-formyltetrahydrofolate cyclo-ligase cog/ cog
ATP binding go/ molecular_function
folic acid-containing compound biosynthetic process go/ biological_process
5-formyltetrahydrofolate cyclo-ligase activity go/ molecular_function
One carbon pool by folate kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
MTHFS_bact tigr/ tigrfam
Module neighborhood information for BC4262

BC4262 has total of 39 gene neighbors in modules 41, 394
Gene neighbors (39)
Gene Common Name Description Module membership
BC0046 BC0046 Dimethyladenosine transferase (NCBI ptt file) 285, 394
BC0057 BC0057 hypothetical protein (NCBI ptt file) 243, 394
BC0065 BC0065 Cell division protein DIVIC (NCBI ptt file) 41, 275
BC0107 BC0107 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (NCBI ptt file) 285, 394
BC0188 BC0188 Phosphoglucosamine mutase (NCBI ptt file) 394, 455
BC0289 BC0289 O-sialoglycoprotein endopeptidase (RefSeq) 22, 394
BC0453 BC0453 Zinc uptake P-type ATPase (NCBI ptt file) 118, 394
BC0509 BC0509 Multidrug resistance ABC transporter ATP-binding and permease protein (NCBI ptt file) 394, 414
BC0539 BC0539 hypothetical protein (RefSeq) 41, 169
BC0544 BC0544 iron-sulfur cluster-binding protein (NCBI ptt file) 394, 476
BC0840 BC0840 Transcriptional regulator, RpiR family (NCBI ptt file) 41, 261
BC1023 BC1023 Transporter, LysE family (NCBI ptt file) 41, 480
BC1298 BC1298 Carbohydrate diacid regulator (NCBI ptt file) 41, 261
BC1744 BC1744 SWF/SNF family helicase (NCBI ptt file) 41, 406
BC1934 BC1934 hypothetical protein (NCBI ptt file) 41, 180
BC2295 BC2295 Exonuclease SbcD (NCBI ptt file) 41, 193
BC2447 BC2447 Chloramphenicol acetyltransferase (NCBI ptt file) 41, 98
BC2748 BC2748 Integral membrane protein (NCBI ptt file) 41, 228
BC2886 BC2886 hypothetical protein (NCBI ptt file) 41, 354
BC3378 BC3378 Luciferase-like monooxygenase (NCBI ptt file) 306, 394
BC3410 BC3410 D-threo-aldose 1-dehydrogenase (NCBI ptt file) 228, 394
BC3499 BC3499 hypothetical Cytosolic Protein (NCBI ptt file) 117, 394
BC3611 BC3611 DNA polymerase III alpha subunit (NCBI ptt file) 41, 261
BC3969 BC3969 hypothetical protein (NCBI ptt file) 394, 479
BC4132 BC4132 None 15, 394
BC4262 BC4262 5-formyltetrahydrofolate cyclo-ligase (NCBI ptt file) 41, 394
BC4321 BC4321 DNA polymerase III, delta subunit (NCBI ptt file) 41, 273
BC4394 BC4394 ATPase, AAA family (NCBI ptt file) 122, 394
BC4426 BC4426 hypothetical Cytosolic Protein (NCBI ptt file) 170, 394
BC4505 BC4505 Transcriptional regulator (NCBI ptt file) 41, 261
BC4562 BC4562 23S rRNA methyltransferase (NCBI ptt file) 41, 261
BC4568 BC4568 Multidrug resistance protein B (NCBI ptt file) 285, 394
BC4589 BC4589 Alkaline phosphatase synthesis two-component response regulator phoP (NCBI ptt file) 41, 527
BC4727 BC4727 hypothetical protein (NCBI ptt file) 41, 385
BC4728 BC4728 Molybdopterin biosynthesis MoeB protein (NCBI ptt file) 41, 90
BC5028 BC5028 Two-component response regulator vanRB (NCBI ptt file) 6, 41
BC5067 BC5067 CrcB family protein (NCBI ptt file) 285, 394
BC5352 BC5352 two-component response regulator YocG (NCBI) 41, 440
BC5353 BC5353 Two-component sensor kinase yocF (NCBI ptt file) 41, 440
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 BC4262
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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