Organism : Methanococcus maripaludis S2 | Module List :
MMP0340 pycB

pyruvate carboxylase subunit B

CircVis
Functional Annotations (10)
Function System
Pyruvate/oxaloacetate carboxyltransferase cog/ cog
pyruvate carboxylase activity go/ molecular_function
sodium ion transport go/ biological_process
metabolic process go/ biological_process
oxaloacetate decarboxylase activity go/ molecular_function
Citrate cycle (TCA cycle) kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
oadA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0340
(Mouseover regulator name to see its description)

MMP0340 is regulated by 18 influences and regulates 0 modules.
Regulators for MMP0340 pycB (18)
Regulator Module Operator
MMP0033 141 tf
MMP0607 141 tf
MMP0907
MMP1646
141 combiner
MMP1704 141 tf
MMP0033 149 tf
MMP0052
MMP0480
149 combiner
MMP0607 149 tf
MMP0637
MMP0678
149 combiner
MMP1467
MMP1646
149 combiner
MMP1704 149 tf
MMP0907
MMP1646
24 combiner
MMP1065 24 tf
MMP1499
MMP1646
24 combiner
MMP1704 24 tf
MMP0568 86 tf
MMP0907
MMP1646
86 combiner
MMP1065 86 tf
MMP1499
MMP1646
86 combiner

Warning: MMP0340 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 10 motifs predicted.

Motif Table (10)
Motif Id e-value Consensus Motif Logo
709 4.70e-04 taCCaCCa
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710 4.30e+03 GCGAGGG
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831 2.30e-01 AaCGagGGgga
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832 7.00e+02 GGCcTTGGCc
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893 1.40e+04 GCGAaGG
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894 1.40e+04 CGtCAGC
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933 7.10e+01 ATctctAtTcTttacATtcc
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934 6.20e+03 GCAAATCATATTTGGTTTCATAC
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947 6.00e-01 taTTaa.cggtGgt
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948 1.50e+02 tCTgtcc.tct.gga.gcat
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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 MMP0340

MMP0340 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Pyruvate/oxaloacetate carboxyltransferase cog/ cog
pyruvate carboxylase activity go/ molecular_function
sodium ion transport go/ biological_process
metabolic process go/ biological_process
oxaloacetate decarboxylase activity go/ molecular_function
Citrate cycle (TCA cycle) kegg/ kegg pathway
Pyruvate metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
oadA tigr/ tigrfam
Module neighborhood information for MMP0340

MMP0340 has total of 84 gene neighbors in modules 24, 86, 120, 141, 149
Gene neighbors (84)
Gene Common Name Description Module membership
MMP0013 argH argininosuccinate lyase 52, 120
MMP0034 GTP cyclohydrolase 130, 149
MMP0073 argG argininosuccinate synthase 27, 120
MMP0076 deoxyribonuclease 24, 35
MMP0100 Na(+)/H(+) exchanger family protein 86, 162
MMP0133 guaB inosine-5'-monophosphate dehydrogenase 25, 120, 140
MMP0134 hypothetical protein MMP0134 24, 92
MMP0137 dys putative deoxyhypusine synthase 25, 141, 149
MMP0160 ftsA-2 coenzyme F390 synthetase 27, 86
MMP0223 hypothetical protein MMP0223 120, 130
MMP0284 infB translation initiation factor IF-2 25, 149
MMP0285 TrkA-N domain-containing protein 80, 86
MMP0287 CBS domain-containing protein 80, 86
MMP0319 cbiL precorrin-2 C-20 methyltransferase 24, 140, 141, 149
MMP0320 shikimate kinase 47, 141
MMP0340 pycB pyruvate carboxylase subunit B 24, 86, 120, 141, 149
MMP0341 pycA pyruvate carboxylase subunit A 67, 86, 120
MMP0415 O-sialoglycoprotein endopeptidase/protein kinase 47, 149
MMP0419 sodium:neurotransmitter symporter 24, 38
MMP0564 hypothetical protein MMP0564 111, 149
MMP0590 glycosyl transferase family protein 35, 86
MMP0637 ArsR family transcriptional regulator 24, 107
MMP0655 hypothetical protein MMP0655 24, 38, 52
MMP0679 Na+/H+ antiporter-like protein 24, 38
MMP0694 beta-lactamase-like protein 51, 109, 149
MMP0702 hypothetical protein MMP0702 24, 38, 162
MMP0713 iorA2 indolepyruvate oxidoreductase subunit alpha 2 24, 47, 86
MMP0714 iorB2 indolepyruvate oxidoreductase subunit beta 24, 47, 86
MMP0715 coenzyme F390 synthetase II 24, 86
MMP0814 hypothetical protein MMP0814 24, 86
MMP0815 hypothetical protein MMP0815 24, 86
MMP0880 aksF isopropylmalate/isohomocitrate dehydrogenase 24, 60, 140, 143
MMP0905 hypothetical protein MMP0905 14, 149
MMP0906 ribonuclease Z 129, 149
MMP0907 transcriptional regulator TrmB 14, 149
MMP0910 hypothetical protein MMP0910 38, 86, 122
MMP0919 dihydroorotate dehydrogenase electron transfer subunit 86, 141
MMP0920 ahcY S-adenosyl-L-homocysteine hydrolase 80, 141
MMP0921 RNAse P, Rpr2/Rpp21 subunit 25, 141
MMP0941 hypothetical protein MMP0941 129, 149
MMP0953 cbiH precorrin-3B C17-methyltransferase 24, 25, 149
MMP0955 sucD succinyl-CoA synthetase subunit alpha 60, 120
MMP0989 top6B DNA topoisomerase VI subunit B 139, 141
MMP1014 radical SAM domain-containing protein 25, 141
MMP1017 lysC aspartate kinase 24, 60, 112
MMP1085 hypothetical protein MMP1085 141, 143, 149
MMP1086 hypothetical protein MMP1086 122, 141
MMP1101 acetylornithine aminotransferase 27, 120
MMP1107 Signal recognition particle protein SRP19 111, 141
MMP1108 corA magnesium/cobalt transporter CorA 141, 149
MMP1112 hypothetical protein MMP1112 111, 129, 141, 149
MMP1113 transketoloase, C terminal half 96, 120
MMP1114 rpe Pentose-5-phosphate 3-epimerase 109, 120
MMP1115 transketolase, N terminal half 109, 120
MMP1128 ppiB cyclophilin type peptidyl-prolyl cis-trans isomerase 47, 86
MMP1196 hypothetical protein MMP1196 27, 86
MMP1222 radA DNA repair and recombination protein RadA 86, 120
MMP1253 hypothetical protein MMP1253 52, 120
MMP1254 purM phosphoribosylaminoimidazole synthetase 96, 120
MMP1255 pheT phenylalanyl-tRNA synthetase subunit beta 60, 120
MMP1270 bifunctional hexulose-6-phosphate synthase/ribonuclease regulator 24, 38
MMP1307 methyltransferase-like protein 4, 149
MMP1313 fen-1 flap endonuclease-1 47, 52, 141
MMP1314 phosphoesterase domain-containing protein 52, 120
MMP1316 korB 2-oxoglutarate ferredoxin oxidoreductase subunit beta 7, 120, 137
MMP1327 rpoK RNA polymerase Rpb6 103, 139, 149
MMP1328 enolase 103, 139, 149
MMP1356 PP-loop domain-containing protein 25, 129, 139, 140, 149
MMP1357 hypothetical protein MMP1357 140, 149
MMP1361 rpoB2 DNA-directed RNA polymerase subunit beta'' 25, 92, 109, 149
MMP1363 rpoA1 DNA-directed RNA polymerase subunit A' 24, 103, 130
MMP1491 trzA amidohydrolase 14, 111, 122, 149
MMP1492 pyrE orotate phosphoribosyltransferase 14, 149
MMP1532 pgk phosphoglycerate kinase 120, 137
MMP1537 cytochrome c heme-binding site 24, 29
MMP1538 transporter component 24, 29
MMP1540 hypothetical protein MMP1540 24, 140
MMP1541 hypothetical protein MMP1541 24, 38
MMP1582 pdaD pyruvoyl-dependent arginine decarboxylase 87, 149
MMP1590 ExsB family protein 24, 51
MMP1614 hisS histidyl-tRNA synthetase 141, 149
MMP1659 pyrB aspartate carbamoyltransferase catalytic subunit 24, 111, 122
Unanno_2 None 24, 86
Unanno_4 None 24, 86
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 MMP0340
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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