Organism : Methanococcus maripaludis S2 | Module List :
MMP0142

thiamine pyrophosphate dependent protein

CircVis
Functional Annotations (10)
Function System
Thiamine pyrophosphate-requiring enzymes [acetolactate synthase, pyruvate dehydrogenase (cytochrome), glyoxylate carboligase, phosphonopyruvate decarboxylase] cog/ cog
magnesium ion binding go/ molecular_function
acetolactate synthase activity go/ molecular_function
thiamine pyrophosphate binding go/ molecular_function
Valine leucine and isoleucine biosynthesis kegg/ kegg pathway
Butanoate metabolism kegg/ kegg pathway
C5-Branched dibasic acid metabolism kegg/ kegg pathway
Pantothenate and CoA biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0142
(Mouseover regulator name to see its description)

MMP0142 is regulated by 13 influences and regulates 0 modules.
Regulators for MMP0142 (13)
Regulator Module Operator
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
MMP1275 17 tf
MMP0036
MMP0840
51 combiner
MMP0052
MMP0257
51 combiner
MMP0097 51 tf
MMP1015 51 tf
MMP1347
Formate
51 combiner

Warning: MMP0142 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
695 1.00e+02 AttTaTAAtGATTAATcaTGAca
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696 1.10e+02 ATAT.GcTgAATaaaAtAGg
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743 1.60e+02 gctgCTGaAAc
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744 1.00e+02 TAttgtggA.aaaataGGG
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763 7.30e+03 CTGCTaCTGAGG
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764 2.80e+04 GcACCTGTtG
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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 MMP0142

MMP0142 is enriched for 10 functions in 3 categories.
Module neighborhood information for MMP0142

MMP0142 has total of 71 gene neighbors in modules 17, 41, 51
Gene neighbors (71)
Gene Common Name Description Module membership
MMP0026 DP2 DNA polymerase II large subunit 25, 41, 92
MMP0046 hypothetical protein MMP0046 20, 51, 140
MMP0074 hypothetical protein MMP0074 51, 140
MMP0091 hypothetical protein MMP0091 51, 106
MMP0108 ABC-type Iron(III)-binding periplasmic protein precursor 41, 67, 95
MMP0116 argC N-acetyl-gamma-glutamyl-phosphate reductase 8, 51
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
MMP0147 nitrogenase reductase-like protein 17, 22
MMP0148 acsA acetyl-CoA synthetase 17, 124
MMP0216 cation transport ATPase 4, 41, 95
MMP0268 truA tRNA pseudouridine synthase A 49, 51
MMP0286 hypothetical protein MMP0286 29, 51
MMP0348 GPR1/FUN34/yaaH family protein 17, 124
MMP0440 DNA-directed RNA polymerase subunit E' 51, 61
MMP0441 rpoE2 DNA-directed RNA polymerase subunit E 51, 61
MMP0442 hypothetical protein MMP0442 3, 51, 61
MMP0443 rps24e 30S ribosomal protein S24e 3, 51, 96, 97
MMP0444 30S ribosomal protein S27ae 3, 51, 97
MMP0493 cobN cobaltochelatase subunit CobN 41, 44
MMP0610 tgtA 7-cyano-7-deazaguanine tRNA-ribosyltransferase 25, 41
MMP0670 hypothetical protein MMP0670 41, 51
MMP0671 ywbE hypothetical protein MMP0671 51, 87
MMP0694 beta-lactamase-like protein 51, 109, 149
MMP0695 psmB proteasome subunit beta 51, 92
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
MMP0884 hypothetical protein MMP0884 39, 51
MMP0901 ATP/GTP-binding motif-containing protein 20, 51
MMP0977 CooC CO dehydrogenase maturation factor 17, 124
MMP0978 hypothetical protein MMP0978 17, 124
MMP0979 hypothetical protein MMP0979 17, 124
MMP0980 cdh acetyl-CoA decarbonylase/synthase complex subunit gamma 17, 124
MMP0981 cdhD acetyl-CoA decarbonylase/synthase complex subunit delta 17, 124
MMP0982 hypothetical protein MMP0982 17, 124
MMP0983 cdhB acetyl-CoA decarbonylase/synthase complex subunit beta 17, 124
MMP0984 cdh acetyl-CoA decarbonylase/synthase complex subunit epsilon 10, 17
MMP0985 cdhA acetyl-CoA decarbonylase/synthase complex subunit alpha 10, 17
MMP1064 adenylate cyclase 4, 51
MMP1074 ehbD hypothetical protein MMP1074 17, 106
MMP1150 mtaA uroporphyrinogen decarboxylase 4, 41, 95
MMP1200 lysA diaminopimelate decarboxylase 21, 41
MMP1271 vorA 2-oxoisovalerate oxidoreductase subunit alpha 10, 17
MMP1274 AMP-dependent synthetase and ligase 10, 17
MMP1334 solute-binding protein/glutamate receptor 41, 129
MMP1380 chlorohydrolase 51, 92
MMP1381 beta-lactamase-like protein 51, 92
MMP1399 aspartate/glutamate/uridylate kinase 51, 61
MMP1431 2pgk 2-phosphoglycerate kinase 49, 51
MMP1432 purA adenylosuccinate synthetase 29, 51, 130
MMP1441 mobB putative molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein 41, 89
MMP1444 methionine aminopeptidase 20, 51, 61, 92
MMP1468 hypothetical protein MMP1468 17, 124
MMP1502 porF hypothetical protein MMP1502 10, 17
MMP1503 porE pyruvate oxidoreductase-associated 10, 17
MMP1504 porB pyruvate ferredoxin oxidoreductase subunit beta 10, 17
MMP1505 porA pyruvate oxidoreductase (synthase) subunit alpha 10, 17
MMP1506 porD pyruvate oxidoreductase (synthase) subunit delta 10, 17
MMP1507 porC pyruvate ferredoxin oxidoreductase subunit gamma 10, 17
MMP1585 arginase 41, 112
MMP1590 ExsB family protein 24, 51
MMP1594 hypothetical protein MMP1594 51, 143
MMP1612 hypothetical protein MMP1612 41, 95
MMP1651 modA molybdenum ABC transporter periplasmic molybdate-binding protein 41, 95
MMP1700 SSS sodium solute transporter superfamily 39, 41
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 MMP0142
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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