Organism : Methanococcus maripaludis S2 | Module List :
MMP1105 sucC

succinate-CoA ligase (ADP-forming), beta chain

CircVis
Functional Annotations (13)
Function System
Succinyl-CoA synthetase, beta subunit cog/ cog
succinate-CoA ligase (ADP-forming) activity go/ molecular_function
ATP binding go/ molecular_function
metabolic process go/ biological_process
succinate-CoA ligase complex (ADP-forming) go/ cellular_component
Citrate cycle (TCA cycle) kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
C5-Branched dibasic acid metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
sucCoAbeta tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1105
(Mouseover regulator name to see its description)

MMP1105 is regulated by 16 influences and regulates 0 modules.
Regulators for MMP1105 sucC (16)
Regulator Module Operator
H2 81 ef
MMP0020 81 tf
MMP0020
MMP0752
81 combiner
MMP0020
MMP0791
81 combiner
MMP0052 81 tf
MMP0052
MMP0480
81 combiner
MMP0168
MMP1100
81 combiner
MMP0637 81 tf
MMP1015 81 tf
MMP1376 81 tf
MMP1467
MMP1646
81 combiner
H2 7 ef
MMP0033
H2
7 combiner
MMP0386
H2
7 combiner
MMP0568
H2
7 combiner
H2 137 ef

Warning: MMP1105 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
675 1.60e-01 GGTGgaA
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676 2.40e+03 cAGtTAGgTTAgTTCgAgTaGT
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823 6.40e-01 GGTGAttT
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824 1.90e+04 cggTTTTacgTaG
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925 2.30e+03 GTTCGATtg.g..TCT.g.ctC
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926 5.30e+03 AAACaAtGtTTtattaTacg
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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 MMP1105

MMP1105 is enriched for 13 functions in 3 categories.
Enrichment Table (13)
Function System
Succinyl-CoA synthetase, beta subunit cog/ cog
succinate-CoA ligase (ADP-forming) activity go/ molecular_function
ATP binding go/ molecular_function
metabolic process go/ biological_process
succinate-CoA ligase complex (ADP-forming) go/ cellular_component
Citrate cycle (TCA cycle) kegg/ kegg pathway
Propanoate metabolism kegg/ kegg pathway
C5-Branched dibasic acid metabolism kegg/ kegg pathway
Carbon fixation pathways in prokaryotes kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
sucCoAbeta tigr/ tigrfam
Module neighborhood information for MMP1105

MMP1105 has total of 62 gene neighbors in modules 7, 81, 137
Gene neighbors (62)
Gene Common Name Description Module membership
MMP0080 glutamate synthase large subunit 7, 60
MMP0145 hpt adenine phosphoribosyltransferase 137, 143
MMP0146 hypothetical protein MMP0146 17, 41, 137
MMP0187 thiC thiamine biosynthesis protein ThiC 137, 143
MMP0212 glycyl-tRNA synthetase 81, 107
MMP0282 purE phosphoribosylaminoimidazole carboxylase catalytic subunit 7, 140
MMP0297 aIF-2_beta translation initiation factor IF-2 subunit beta 60, 81
MMP0308 SirA family protein 7, 78
MMP0318 ilvD dihydroxy-acid dehydratase 7, 40
MMP0326 metG methionyl-tRNA synthetase 7, 40
MMP0345 hypothetical protein MMP0345 7, 70
MMP0346 2-hydroxyglutaryl-CoA dehydratase subunit D-like protein 7, 140
MMP0359 glycosyl transferase family protein 7, 78
MMP0404 cofD 2-phospho-L-lactate transferase 87, 137
MMP0408 H+-transporting two-sector ATPase subunit A 7, 40
MMP0414 thrS threonyl-tRNA synthetase 8, 81, 112
MMP0417 hisA 1-(5-phosphoribosyl)-5- 60, 137
MMP0418 carbohydrate kinase PfkB 60, 137, 143
MMP0539 leuB multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase 7, 8
MMP0541 serB phosphoserine phosphatase SerB 7, 40, 139, 140
MMP0550 amino acid ABC transporter periplasmic protein 81, 140
MMP0588 dph5 diphthine synthase 25, 81, 140
MMP0596 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit 20, 81
MMP0597 flpA fibrillarin 8, 16, 81
MMP0606 ribosomal RNA methyltransferase RrmJ/FtsJ 137, 143
MMP0607 nrpR hypothetical protein MMP0607 115, 137, 143
MMP0666 Na/Pi-cotransporter II-like protein 7, 115
MMP0696 proS prolyl-tRNA synthetase 7, 60
MMP0708 hypothetical protein MMP0708 7, 40
MMP0881 hypothetical protein MMP0881 111, 137
MMP0893 pyrG CTP synthetase 7, 60
MMP0899 ATP/GTP-binding motif-containing protein 70, 81
MMP0900 rhodanese domain-containing protein 70, 81
MMP0946 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B 8, 81, 96
MMP0947 hisG ATP phosphoribosyltransferase 7, 40
MMP1018 cimA (R)-citramalate synthase 7, 27
MMP1063 leuA 2-isopropylmalate synthase 81, 143
MMP1068 K+-dependent Na+/Ca+ exchanger related-protein:Sodium/calcium exchanger membrane region 81, 140
MMP1081 wbpG putative LPS biosynthesis protein WbpG 137, 143
MMP1083 imidazole glycerol phosphate synthase subunit HisF 137, 143
MMP1105 sucC succinate-CoA ligase (ADP-forming), beta chain 7, 81, 137
MMP1106 hypothetical protein MMP1106 81, 137, 140
MMP1122 translation-associated GTPase 137, 143
MMP1131 peptide chain release factor 1 20, 81
MMP1146 purF amidophosphoribosyltransferase 7, 60, 137, 143
MMP1206 glnA glutamine synthetase 99, 137
MMP1242 nadA quinolinate synthetase 27, 81
MMP1266 glutamyl-tRNA(Gln) amidotransferase subunit D 7, 40, 68
MMP1315 korG 2-oxoglutarate ferredoxin oxidoreductase subunit gamma 7, 80
MMP1316 korB 2-oxoglutarate ferredoxin oxidoreductase subunit beta 7, 120, 137
MMP1352 ribulose-1,5-biphosphate synthetase 7, 8, 78
MMP1353 hypothetical protein MMP1353 81, 140
MMP1427 hypothetical protein MMP1427 81, 112
MMP1440 tRNA-modifying protein 129, 137
MMP1470 pdfA prefoldin subunit alpha 7, 111
MMP1496 pheS phenylalanyl-tRNA synthetase subunit alpha 137, 143
MMP1532 pgk phosphoglycerate kinase 120, 137
MMP1587 hypothetical protein MMP1587 7, 14, 80
MMP1588 serA D-3-phosphoglycerate dehydrogenase 7, 8, 27, 77
MMP1589 carA carbamoyl phosphate synthase small subunit 7, 78
MMP1615 hypothetical protein MMP1615 7, 112
MMP1656 glutamine amidotransferase subunit PdxT 8, 137
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 MMP1105
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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