Organism : Methanococcus maripaludis S2 | Module List :
MMP0330 cbiC

precorrin-8X methylmutase

CircVis
Functional Annotations (5)
Function System
Precorrin isomerase cog/ cog
cobalamin biosynthetic process go/ biological_process
precorrin-8X methylmutase activity go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0330
(Mouseover regulator name to see its description)

MMP0330 is regulated by 19 influences and regulates 0 modules.
Regulators for MMP0330 cbiC (19)
Regulator Module Operator
MMP0033
MMP0480
68 combiner
MMP0097
H2
68 combiner
MMP0402
MMP0629
68 combiner
MMP0907
H2
68 combiner
MMP1499
H2
68 combiner
MMP0033 122 tf
MMP0033
MMP0386
122 combiner
MMP0168
MMP0907
122 combiner
MMP0168
MMP1499
122 combiner
MMP0386
MMP0607
122 combiner
MMP0607 122 tf
MMP1052
MMP1499
122 combiner
MMP0033 157 tf
MMP0033
MMP0386
157 combiner
MMP0168
MMP0907
157 combiner
MMP0168
MMP1499
157 combiner
MMP0386
MMP0402
157 combiner
MMP0607 157 tf
MMP0787
MMP1499
157 combiner

Warning: MMP0330 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 6 motifs predicted.

Motif Table (6)
Motif Id e-value Consensus Motif Logo
797 9.40e-02 AAtTCAcCgc
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798 3.50e+01 gttTtTaTgTAgGTaAg
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897 7.50e+00 AAtggCGGTG
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898 7.10e+02 cGgaaATtccg
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963 2.10e+02 cca.C.gCat.tCcgCtttc.
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964 2.40e+03 CCCtCC
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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 MMP0330

MMP0330 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Precorrin isomerase cog/ cog
cobalamin biosynthetic process go/ biological_process
precorrin-8X methylmutase activity go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Module neighborhood information for MMP0330

MMP0330 has total of 48 gene neighbors in modules 68, 122, 157
Gene neighbors (48)
Gene Common Name Description Module membership
MMP0131 L-tyrosine decarboxylase 111, 122, 129, 157
MMP0185 mtaP 5'-methylthioadenosine phosphorylase 122, 157
MMP0222 hypothetical protein MMP0222 14, 122, 157
MMP0230 metal dependent phosphohydrolase 40, 68
MMP0251 psmA proteasome subunit alpha 46, 68
MMP0291 hydrogenase expression/formation protein-like protein 47, 122
MMP0325 glyceraldehyde-3-phosphate dehydrogenase 68, 111
MMP0328 hypothetical protein MMP0328 15, 157
MMP0329 hypothetical protein MMP0329 122, 157
MMP0330 cbiC precorrin-8X methylmutase 68, 122, 157
MMP0357 UDP-N-acetylglucosamine 2-epimerase 139, 157
MMP0358 hypothetical protein MMP0358 139, 157
MMP0388 geranylgeranyl reductase 39, 68
MMP0389 ferredoxin 39, 68
MMP0390 hypothetical protein MMP0390 15, 157
MMP0428 vanadium nitrogenase-associated-like protein N 14, 68
MMP0516 modD quinolinate phosphoribosyl transferase 46, 68
MMP0582 AzlC family protein 47, 68
MMP0583 branched chain amino acid ABC transporter 40, 68
MMP0706 NAD binding site:UDP-glucose/GDP-mannose dehydrogenase 111, 157
MMP0872 hemC porphobilinogen deaminase 40, 68
MMP0910 hypothetical protein MMP0910 38, 86, 122
MMP0926 cheB response regulator receiver modulated CheB methylesterase 68, 98, 164
MMP0938 cobS cobalamin (5'-phosphate) synthase 47, 122
MMP0966 cobA uroporphyrin-III C-methyltransferase 68, 70
MMP1024 MCE family-like protein 14, 47, 157
MMP1032 rpa replication factor A 40, 68
MMP1033 hypothetical protein MMP1033 68, 99
MMP1034 tmk thymidylate kinase 66, 68
MMP1075 dut dUTP diphosphatase 40, 68
MMP1076 hexapeptide repeat-containing transferase 40, 68
MMP1077 phosphoglucomutase/phosphomannomutase 40, 68, 139
MMP1086 hypothetical protein MMP1086 122, 141
MMP1121 metal-dependent phophohydrolase-like protein 129, 157
MMP1132 endA tRNA-splicing endonuclease subunit alpha 122, 157
MMP1133 comC L-sulfolactate dehydrogenase/(S)-hydroxyglutaric acid dehydrogenase 122, 157
MMP1204 M24 family metallopeptidase 15, 68
MMP1205 aroA 3-phosphoshikimate 1-carboxyvinyltransferase 40, 68
MMP1264 hypothetical protein MMP1264 104, 142, 157
MMP1266 glutamyl-tRNA(Gln) amidotransferase subunit D 7, 40, 68
MMP1344 hypothetical protein MMP1344 111, 157
MMP1491 trzA amidohydrolase 14, 111, 122, 149
MMP1500 ftsz2 cell division protein FtsZ 139, 157
MMP1521 hypothetical protein MMP1521 14, 111, 122, 157
MMP1659 pyrB aspartate carbamoyltransferase catalytic subunit 24, 111, 122
MMP1674 flaH flagellar accessory protein FlaH 68, 98
MMP1675 flaI type II secretion system protein E 68, 98, 164
MMP1676 flaJ flagellar assembly protein J 68, 98
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 MMP0330
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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