Organism : Methanococcus maripaludis S2 | Module List :
MMP0131

L-tyrosine decarboxylase

CircVis
Functional Annotations (10)
Function System
Glutamate decarboxylase and related PLP-dependent proteins cog/ cog
biosynthetic process go/ biological_process
transferase activity, transferring nitrogenous groups go/ molecular_function
carboxy-lyase activity go/ molecular_function
carboxylic acid metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Tyrosine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
tyr_de_CO2_Arch tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0131
(Mouseover regulator name to see its description)

MMP0131 is regulated by 21 influences and regulates 0 modules.
Regulators for MMP0131 (21)
Regulator Module Operator
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
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
MMP1447 111 tf
MMP0168
MMP0907
129 combiner
MMP0637 129 tf
MMP0787
MMP0907
129 combiner
MMP1023
MMP1303
129 combiner
MMP1303
H2
129 combiner
MMP1376
H2
129 combiner

Warning: MMP0131 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 8 motifs predicted.

Motif Table (8)
Motif Id e-value Consensus Motif Logo
879 7.70e+01 atGGTG
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880 2.90e+02 gCATCAATCAAAATcTagcgA
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897 7.50e+00 AAtggCGGTG
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898 7.10e+02 cGgaaATtccg
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911 2.10e+03 tccGCCAC
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912 2.40e+04 CCacACcGTGC
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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 MMP0131

MMP0131 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Glutamate decarboxylase and related PLP-dependent proteins cog/ cog
biosynthetic process go/ biological_process
transferase activity, transferring nitrogenous groups go/ molecular_function
carboxy-lyase activity go/ molecular_function
carboxylic acid metabolic process go/ biological_process
pyridoxal phosphate binding go/ molecular_function
Tyrosine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
tyr_de_CO2_Arch tigr/ tigrfam
Module neighborhood information for MMP0131

MMP0131 has total of 61 gene neighbors in modules 111, 122, 129, 157
Gene neighbors (61)
Gene Common Name Description Module membership
Antisense_13 None 49, 129
MMP0036 tfe transcription initiation factor E subunit alpha 49, 87, 92, 129
MMP0072 hypothetical protein MMP0072 28, 129
MMP0078 hypothetical protein MMP0078 12, 111
MMP0079 orotate phosphoribosyltransferase-like protein 12, 111
MMP0131 L-tyrosine decarboxylase 111, 122, 129, 157
MMP0185 mtaP 5'-methylthioadenosine phosphorylase 122, 157
MMP0222 hypothetical protein MMP0222 14, 122, 157
MMP0264 MscMJ mechanosensitive ion channel MscS 129, 143
MMP0265 hypothetical protein MMP0265 28, 129
MMP0291 hydrogenase expression/formation protein-like protein 47, 122
MMP0296 hypothetical protein MMP0296 4, 129
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
MMP0390 hypothetical protein MMP0390 15, 157
MMP0554 SAM-binding motif-containing protein 129, 140
MMP0561 cmd carboxymuconolactone decarboxylase 52, 111
MMP0564 hypothetical protein MMP0564 111, 149
MMP0580 act anaerobic ribonucleoside-triphosphate reductase activating protein 115, 129
MMP0602 pyrF orotidine-5'-phosphate decarboxylase 12, 111
MMP0706 NAD binding site:UDP-glucose/GDP-mannose dehydrogenase 111, 157
MMP0876 cofG FO synthase subunit 1 1, 129
MMP0881 hypothetical protein MMP0881 111, 137
MMP0883 hypothetical protein MMP0883 115, 129
MMP0906 ribonuclease Z 129, 149
MMP0910 hypothetical protein MMP0910 38, 86, 122
MMP0938 cobS cobalamin (5'-phosphate) synthase 47, 122
MMP0941 hypothetical protein MMP0941 129, 149
MMP0942 hypothetical protein MMP0942 111, 115
MMP0943 taqD glycerol-3-phosphate cytidyltransferase 92, 111
MMP0970 lig DNA ligase I, ATP-dependent Dnl1 47, 129
MMP1011 gltX glutamyl-tRNA synthetase 25, 129
MMP1024 MCE family-like protein 14, 47, 157
MMP1086 hypothetical protein MMP1086 122, 141
MMP1107 Signal recognition particle protein SRP19 111, 141
MMP1109 hypothetical protein MMP1109 111, 129
MMP1112 hypothetical protein MMP1112 111, 129, 141, 149
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
MMP1264 hypothetical protein MMP1264 104, 142, 157
MMP1265 glutamyl-tRNA(Gln) amidotransferase subunit E 28, 129
MMP1334 solute-binding protein/glutamate receptor 41, 129
MMP1344 hypothetical protein MMP1344 111, 157
MMP1345 undecaprenyl pyrophospahte synthetase-like protein 49, 111
MMP1356 PP-loop domain-containing protein 25, 129, 139, 140, 149
MMP1440 tRNA-modifying protein 129, 137
MMP1467 ehaT hypothetical protein MMP1467 28, 129, 133
MMP1470 pdfA prefoldin subunit alpha 7, 111
MMP1491 trzA amidohydrolase 14, 111, 122, 149
MMP1500 ftsz2 cell division protein FtsZ 139, 157
MMP1521 hypothetical protein MMP1521 14, 111, 122, 157
MMP1600 ribosomal protein S6 modification protein 104, 129
MMP1630 ABC transporter ATPase 129, 133
MMP1659 pyrB aspartate carbamoyltransferase catalytic subunit 24, 111, 122
MMP1722 hisF imidazole glycerol phosphate synthase subunit HisF 111, 115
Unanno_61 None 111, 129
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 MMP0131
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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