Organism : Methanococcus maripaludis S2 | Module List :
MMP1200 lysA

diaminopimelate decarboxylase

CircVis
Functional Annotations (8)
Function System
Diaminopimelate decarboxylase cog/ cog
diaminopimelate decarboxylase activity go/ molecular_function
lysine biosynthetic process via diaminopimelate go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
lysA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1200
(Mouseover regulator name to see its description)

MMP1200 is regulated by 10 influences and regulates 0 modules.
Regulators for MMP1200 lysA (10)
Regulator Module Operator
H2 21 ef
MMP0036
H2
21 combiner
MMP1100 21 tf
MMP0036
MMP0217
41 combiner
MMP0036
MMP1023
41 combiner
MMP0217
MMP1303
41 combiner
MMP0480 41 tf
MMP1100 41 tf
MMP1303
H2
41 combiner
MMP1376 41 tf

Warning: MMP1200 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
703 3.80e+03 GGCGaGgc
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704 3.50e+03 CgatTccccCc
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743 1.60e+02 gctgCTGaAAc
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744 1.00e+02 TAttgtggA.aaaataGGG
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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 MMP1200

MMP1200 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Diaminopimelate decarboxylase cog/ cog
diaminopimelate decarboxylase activity go/ molecular_function
lysine biosynthetic process via diaminopimelate go/ biological_process
Lysine biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
lysA tigr/ tigrfam
Module neighborhood information for MMP1200

MMP1200 has total of 56 gene neighbors in modules 21, 41
Gene neighbors (56)
Gene Common Name Description Module membership
MMP0026 DP2 DNA polymerase II large subunit 25, 41, 92
MMP0108 ABC-type Iron(III)-binding periplasmic protein precursor 41, 67, 95
MMP0141 hypothetical protein MMP0141 41, 51
MMP0142 thiamine pyrophosphate dependent protein 17, 41, 51
MMP0144 hpcE 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase 17, 41
MMP0146 hypothetical protein MMP0146 17, 41, 137
MMP0216 cation transport ATPase 4, 41, 95
MMP0228 trm1 N(2),N(2)-dimethylguanosine tRNA methyltransferase 21, 42
MMP0270 Fe-S cluster domain-containing protein 21, 70
MMP0271 putative ATP binding nickel incorporation protein 21, 95
MMP0272 ABC transporter ATPase 21, 70
MMP0273 comA phosphosulfolactate synthase 21, 70
MMP0493 cobN cobaltochelatase subunit CobN 41, 44
MMP0610 tgtA 7-cyano-7-deazaguanine tRNA-ribosyltransferase 25, 41
MMP0618 hypothetical protein MMP0618 21, 70
MMP0619 hypothetical protein MMP0619 21, 70
MMP0620 atwA methyl coenzyme M reductase, component A2 21, 70
MMP0670 hypothetical protein MMP0670 41, 51
MMP0698 hypothetical protein MMP0698 21, 143
MMP0861 kamA lysine 2,3-aminomutase 41, 95
MMP0862 yodP GCN5-like N-acetyltransferase 41, 95
MMP0866 proX glycine betaine ABC transporter substrate-binding protein 41, 89
MMP0867 binding-protein dependent transport system inner membrane protein 41, 89
MMP0868 proV ABC transporter ATPase 41, 66
MMP0904 selD selenophosphate synthetase 21, 70
MMP0954 hypothetical protein MMP0954 21, 70
MMP1021 hypothetical protein MMP1021 8, 21
MMP1022 hypothetical protein MMP1022 21, 70
MMP1023 TetR family transcriptional regulator 8, 21, 78
MMP1026 argS arginyl-tRNA synthetase 12, 21
MMP1150 mtaA uroporphyrinogen decarboxylase 4, 41, 95
MMP1186 lon thiol (cysteine) protease 21, 115
MMP1200 lysA diaminopimelate decarboxylase 21, 41
MMP1259 FAD-dependent pyridine nucleotide-disulfide oxidoreductase 12, 21
MMP1317 hypothetical protein MMP1317 21, 115
MMP1318 lysS lysyl-tRNA synthetase 20, 21
MMP1334 solute-binding protein/glutamate receptor 41, 129
MMP1358 ferredoxin 13, 21
MMP1441 mobB putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein 41, 89
MMP1512 alr alanine racemase 8, 21
MMP1513 ald alanine dehydrogenase 8, 21
MMP1527 aspartate aminotransferase 8, 21
MMP1583 S-adenosylmethionine decarboxylase-like protein 21, 112
MMP1584 spermidine synthase 11, 21
MMP1585 arginase 41, 112
MMP1611 hypothetical protein MMP1611 21, 106
MMP1612 hypothetical protein MMP1612 41, 95
MMP1651 modA molybdenum ABC transporter periplasmic molybdate-binding protein 41, 95
MMP1657 hypothetical protein MMP1657 21, 28
MMP1681 hypothetical protein MMP1681 21, 143
MMP1682 recJ single stranded DNA-specific exonuclease 21, 106
MMP1700 SSS sodium solute transporter superfamily 39, 41
MMP1704 hypothetical protein MMP1704 21, 115
MMP1706 H/ACA RNA-protein complex component Nop10p 20, 21
MMP1707 aIF2_alpha translation initiation factor IF-2 subunit alpha 20, 21
Unanno_28 None 41, 95
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 MMP1200
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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