Organism : Methanococcus maripaludis S2 | Module List :
MMP0541 serB

phosphoserine phosphatase SerB

CircVis
Functional Annotations (8)
Function System
Phosphoserine phosphatase cog/ cog
phosphoserine phosphatase activity go/ molecular_function
L-serine biosynthetic process go/ biological_process
Glycine serine and threonine metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
serB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0541
(Mouseover regulator name to see its description)

MMP0541 is regulated by 23 influences and regulates 0 modules.
Regulators for MMP0541 serB (23)
Regulator Module Operator
MMP0386
MMP0629
40 combiner
MMP0629
MMP0907
40 combiner
MMP0907
H2
40 combiner
MMP1275
H2
40 combiner
H2 7 ef
MMP0033
H2
7 combiner
MMP0386
H2
7 combiner
MMP0568
H2
7 combiner
MMP0033
H2
140 combiner
MMP0033
MMP0629
140 combiner
MMP0052
MMP0257
140 combiner
MMP0637 140 tf
MMP1467
MMP1646
140 combiner
MMP0033 139 tf
MMP0033
H2
139 combiner
MMP0033
MMP0086
139 combiner
MMP0033
MMP0168
139 combiner
MMP0607 139 tf
MMP0631 139 tf
MMP0637 139 tf
MMP0907 139 tf
MMP1442
MMP1467
139 combiner
MMP1704 139 tf

Warning: MMP0541 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
675 1.60e-01 GGTGgaA
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676 2.40e+03 cAGtTAGgTTAgTTCgAgTaGT
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741 3.30e-03 AatTCACCa.
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742 4.00e+04 CCccaGAGG
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929 1.70e+01 T.aGGtgattT
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930 4.20e+01 TgtgctTttTgaa.gcaa.caAc
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931 1.10e-02 aTCTGGTG
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932 1.10e+02 GGGTTCAAATCCCcccCacaGCGC
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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 MMP0541

MMP0541 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Phosphoserine phosphatase cog/ cog
phosphoserine phosphatase activity go/ molecular_function
L-serine biosynthetic process go/ biological_process
Glycine serine and threonine metabolism kegg/ kegg pathway
Methane metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
serB tigr/ tigrfam
Module neighborhood information for MMP0541

MMP0541 has total of 94 gene neighbors in modules 7, 40, 139, 140
Gene neighbors (94)
Gene Common Name Description Module membership
MMP0046 hypothetical protein MMP0046 20, 51, 140
MMP0056 cofH FO synthase subunit 2 14, 139
MMP0074 hypothetical protein MMP0074 51, 140
MMP0080 glutamate synthase large subunit 7, 60
MMP0098 ferredoxin 40, 107
MMP0106 hypothetical protein MMP0106 107, 140
MMP0133 guaB inosine-5'-monophosphate dehydrogenase 25, 120, 140
MMP0152 citrate transporter 14, 139
MMP0210 hypothetical protein MMP0210 58, 140
MMP0220 Sodium/proline symporter-related 70, 140
MMP0224 hemL glutamate-1-semialdehyde aminotransferase 60, 130, 140
MMP0230 metal dependent phosphohydrolase 40, 68
MMP0282 purE phosphoribosylaminoimidazole carboxylase catalytic subunit 7, 140
MMP0308 SirA family protein 7, 78
MMP0318 ilvD dihydroxy-acid dehydratase 7, 40
MMP0319 cbiL precorrin-2 C-20 methyltransferase 24, 140, 141, 149
MMP0326 metG methionyl-tRNA synthetase 7, 40
MMP0345 hypothetical protein MMP0345 7, 70
MMP0346 2-hydroxyglutaryl-CoA dehydratase subunit D-like protein 7, 140
MMP0353 UDP-glucose/GDP-mannose dehydrogenase-like protein 80, 139
MMP0356 group 1 glycosyl transferase 80, 139, 140
MMP0357 UDP-N-acetylglucosamine 2-epimerase 139, 157
MMP0358 hypothetical protein MMP0358 139, 157
MMP0359 glycosyl transferase family protein 7, 78
MMP0393 phosphodiesterase 40, 80
MMP0408 H+-transporting two-sector ATPase subunit A 7, 40
MMP0530 hypothetical protein MMP0530 92, 140
MMP0531 hypothetical protein MMP0531 106, 140
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
MMP0554 SAM-binding motif-containing protein 129, 140
MMP0579 hypothetical protein MMP0579 115, 139
MMP0583 branched chain amino acid ABC transporter 40, 68
MMP0588 dph5 diphthine synthase 25, 81, 140
MMP0609 pth2 peptidyl-tRNA hydrolase 66, 140
MMP0666 Na/Pi-cotransporter II-like protein 7, 115
MMP0696 proS prolyl-tRNA synthetase 7, 60
MMP0705 wbpI UDP-N-acetylglucosamine 2-epimerase 80, 140
MMP0707 sodium/hydrogen exchanger 87, 109, 140
MMP0708 hypothetical protein MMP0708 7, 40
MMP0865 aminotransferase (subgroup II) adenosylmethionine-8-amino-7-oxononanoate aminotransferase 115, 140
MMP0872 hemC porphobilinogen deaminase 40, 68
MMP0878 ribonuclease P-like protein 25, 87, 140
MMP0880 aksF isopropylmalate/isohomocitrate dehydrogenase 24, 60, 140, 143
MMP0887 stress responsive alpha-beta barrel domain-containing protein 40, 136
MMP0893 pyrG CTP synthetase 7, 60
MMP0947 hisG ATP phosphoribosyltransferase 7, 40
MMP0989 top6B DNA topoisomerase VI subunit B 139, 141
MMP0999 hypothetical protein MMP0999 95, 140
MMP1018 cimA (R)-citramalate synthase 7, 27
MMP1032 rpa replication factor A 40, 68
MMP1068 K+-dependent Na+/Ca+ exchanger related-protein:Sodium/calcium exchanger membrane region 81, 140
MMP1075 dut dUTP diphosphatase 40, 68
MMP1076 hexapeptide repeat-containing transferase 40, 68
MMP1077 phosphoglucomutase/phosphomannomutase 40, 68, 139
MMP1105 sucC succinate-CoA ligase (ADP-forming), beta chain 7, 81, 137
MMP1106 hypothetical protein MMP1106 81, 137, 140
MMP1116 cellulase 40, 78
MMP1117 hypothetical protein MMP1117 14, 47, 52, 139
MMP1129 ppiB cyclophilin type peptidyl-prolyl cis-trans isomerase 40, 70, 78
MMP1146 purF amidophosphoribosyltransferase 7, 60, 137, 143
MMP1189 ribose-5-phosphate isomerase A 60, 139
MMP1205 aroA 3-phosphoshikimate 1-carboxyvinyltransferase 40, 68
MMP1260 hypothetical protein MMP1260 40, 96
MMP1266 glutamyl-tRNA(Gln) amidotransferase subunit D 7, 40, 68
MMP1312 hypothetical protein MMP1312 52, 140
MMP1315 korG 2-oxoglutarate ferredoxin oxidoreductase subunit gamma 7, 80
MMP1316 korB 2-oxoglutarate ferredoxin oxidoreductase subunit beta 7, 120, 137
MMP1326 rpoN DNA-directed RNA polymerase subunit N 103, 118, 140
MMP1327 rpoK RNA polymerase Rpb6 103, 139, 149
MMP1328 enolase 103, 139, 149
MMP1352 ribulose-1,5-biphosphate synthetase 7, 8, 78
MMP1353 hypothetical protein MMP1353 81, 140
MMP1356 PP-loop domain-containing protein 25, 129, 139, 140, 149
MMP1357 hypothetical protein MMP1357 140, 149
MMP1362 rpoB1 DNA-directed RNA polymerase subunit B' 63, 130, 140
MMP1425 tRNA 2'-O-methylase 25, 87, 140
MMP1426 dcd bifunctional dCTP deaminase/dUTP diphosphatase 16, 112, 140
MMP1438 hypothetical protein MMP1438 14, 140
MMP1470 pdfA prefoldin subunit alpha 7, 111
MMP1499 hypothetical protein MMP1499 14, 139
MMP1500 ftsz2 cell division protein FtsZ 139, 157
MMP1540 hypothetical protein MMP1540 24, 140
MMP1554 hypothetical protein MMP1554 15, 139
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
MMP1610 hypothetical protein MMP1610 19, 139
MMP1615 hypothetical protein MMP1615 7, 112
MMP1648 hypothetical protein MMP1648 14, 47, 52, 139
MMP1701 amino acid-binding ACT domain-containing protein 27, 40
MMP1702 hom homoserine dehydrogenase 27, 40
MMP1711 pcnA proliferating cell nuclear antigen 115, 139
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 MMP0541
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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