Organism : Methanococcus maripaludis S2 | Module List :
MMP1588 serA

D-3-phosphoglycerate dehydrogenase

CircVis
Functional Annotations (10)
Function System
Phosphoglycerate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
L-serine biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
NAD binding go/ molecular_function
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
PGDH tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1588
(Mouseover regulator name to see its description)

MMP1588 is regulated by 18 influences and regulates 0 modules.
Regulators for MMP1588 serA (18)
Regulator Module Operator
H2 8 ef
MMP0217
MMP1646
8 combiner
MMP0465
Formate
8 combiner
MMP1210
MMP1646
8 combiner
MMP1304 8 tf
MMP0052
MMP1304
27 combiner
MMP0097
MMP0465
27 combiner
MMP0499 27 tf
MMP1304 27 tf
MMP1447 27 tf
H2 7 ef
MMP0033
H2
7 combiner
MMP0386
H2
7 combiner
MMP0568
H2
7 combiner
MMP0052
MMP1304
77 combiner
MMP0499 77 tf
MMP1015 77 tf
MMP1447 77 tf

Warning: MMP1588 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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677 6.30e-02 cccgcaGgTTCaactcccccTccc
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678 8.30e-01 aGGTGATTTT
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715 3.40e-02 GGTGat
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716 2.00e+03 TCGAGcGC.tC
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815 8.70e+01 CACCTc
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816 6.90e+01 cGggggGcT
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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 MMP1588

MMP1588 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Phosphoglycerate dehydrogenase and related dehydrogenases cog/ cog
phosphoglycerate dehydrogenase activity go/ molecular_function
L-serine biosynthetic process go/ biological_process
amino acid binding go/ molecular_function
NAD binding go/ molecular_function
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
PGDH tigr/ tigrfam
Module neighborhood information for MMP1588

MMP1588 has total of 114 gene neighbors in modules 7, 8, 27, 77
Gene neighbors (114)
Gene Common Name Description Module membership
MMP0003 korA 2-oxoglutarate ferredoxin oxidoreductase subunit alpha 27, 77
MMP0006 3-dehydroquinate synthase 27, 77
MMP0025 hypothetical protein MMP0025 8, 52
MMP0059 hypothetical protein MMP0059 8, 58, 64
MMP0061 aIF6 translation initiation factor IF-6 8, 61, 96, 138
MMP0062 50S ribosomal protein L31e 61, 77, 96, 128, 138
MMP0073 argG argininosuccinate synthase 27, 120
MMP0080 glutamate synthase large subunit 7, 60
MMP0093 50S ribosomal protein L21e 8, 11, 20
MMP0094 putative pseudouridylate synthase 8, 11
MMP0103 pyridoxal biosynthesis lyase PdxS 8, 27, 77
MMP0116 argC N-acetyl-gamma-glutamyl-phosphate reductase 8, 51
MMP0127 hmd H(2)-dependent methylenetetrahydromethanopterin dehydrogenase 8, 77
MMP0135 thrC threonine synthase 27, 77
MMP0136 leuD 3-isopropylmalate dehydratase small subunit 27, 77
MMP0160 ftsA-2 coenzyme F390 synthetase 27, 86
MMP0183 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase 8, 70
MMP0242 hypothetical protein MMP0242 8, 39, 96
MMP0249 rpl37ae 50S ribosomal protein L37Ae 61, 77
MMP0250 putative RNA-associated protein 61, 77
MMP0261 DNA directed RNA polymerase subunit L 27, 77
MMP0282 purE phosphoribosylaminoimidazole carboxylase catalytic subunit 7, 140
MMP0290 nac nascent polypeptide-associated complex protein 8, 78
MMP0308 SirA family protein 7, 78
MMP0309 DsrE family protein 8, 78
MMP0317 hypothetical protein MMP0317 77, 96
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
MMP0370 hypothetical protein MMP0370 77, 96
MMP0371 hypothetical protein MMP0371 8, 70
MMP0382 putative ATPase RIL 8, 70, 78
MMP0391 aspC aspartate aminotransferase 77, 78
MMP0396 eno phosphopyruvate hydratase 77, 78
MMP0407 hypothetical protein MMP0407 8, 19, 89
MMP0408 H+-transporting two-sector ATPase subunit A 7, 40
MMP0414 thrS threonyl-tRNA synthetase 8, 81, 112
MMP0539 leuB multifunctional 3-isopropylmalate dehydrogenase/D-malate dehydrogenase 7, 8
MMP0540 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 8, 112, 143
MMP0541 serB phosphoserine phosphatase SerB 7, 40, 139, 140
MMP0553 argF ornithine carbamoyltransferase 27, 77
MMP0597 flpA fibrillarin 8, 16, 81
MMP0629 hypothetical protein MMP0629 8, 39
MMP0645 mdh malate dehydrogenase 8, 39, 136
MMP0650 ilvB acetolactate synthase catalytic subunit 8, 39
MMP0651 ilvH acetolactate synthase 3 regulatory subunit 8, 39
MMP0654 ilvC ketol-acid reductoisomerase 27, 77
MMP0657 hypothetical protein MMP0657 8, 29, 96
MMP0666 Na/Pi-cotransporter II-like protein 7, 115
MMP0687 tpiA triosephosphate isomerase 8, 13
MMP0696 proS prolyl-tRNA synthetase 7, 60
MMP0697 leuS leucyl-tRNA synthetase 8, 143
MMP0704 ParA type ATPase 8, 78, 112
MMP0708 hypothetical protein MMP0708 7, 40
MMP0736 PRC-barrel domain-containing protein 8, 19, 38
MMP0737 L-aspartate dehydrogenase 8, 38
MMP0816 seryl-tRNA synthetase-like protein 8, 70
MMP0879 serS seryl-tRNA synthetase 27, 143
MMP0893 pyrG CTP synthetase 7, 60
MMP0898 cellulose-binding protein 8, 70
MMP0946 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B 8, 81, 96
MMP0947 hisG ATP phosphoribosyltransferase 7, 40
MMP0965 formylmethanofuran dehydrogenase subunit E-like protein 8, 39, 136
MMP0971 purB adenylosuccinate lyase 8, 11
MMP1013 carB carbamoyl-phosphate synthase large subunit 77, 96
MMP1018 cimA (R)-citramalate synthase 7, 27
MMP1021 hypothetical protein MMP1021 8, 21
MMP1023 TetR family transcriptional regulator 8, 21, 78
MMP1035 hypothetical protein MMP1035 77, 136
MMP1036 hypothetical protein MMP1036 77, 136
MMP1070 hypothetical protein MMP1070 8, 15
MMP1101 acetylornithine aminotransferase 27, 120
MMP1105 sucC succinate-CoA ligase (ADP-forming), beta chain 7, 81, 137
MMP1139 thiE thiamine-phosphate pyrophosphorylase 27, 70, 78
MMP1146 purF amidophosphoribosyltransferase 7, 60, 137, 143
MMP1149 leuC 3-isopropylmalate dehydratase large subunit 27, 77
MMP1196 hypothetical protein MMP1196 27, 86
MMP1213 hypothetical protein MMP1213 8, 89
MMP1242 nadA quinolinate synthetase 27, 81
MMP1266 glutamyl-tRNA(Gln) amidotransferase subunit D 7, 40, 68
MMP1308 tal putative translaldolase 8, 16, 112
MMP1310 purO IMP cyclohydrolase 27, 77
MMP1311 ferredoxin 27, 77
MMP1315 korG 2-oxoglutarate ferredoxin oxidoreductase subunit gamma 7, 80
MMP1316 korB 2-oxoglutarate ferredoxin oxidoreductase subunit beta 7, 120, 137
MMP1321 rps11p 30S ribosomal protein S11P 8, 105, 118
MMP1352 ribulose-1,5-biphosphate synthetase 7, 8, 78
MMP1470 pdfA prefoldin subunit alpha 7, 111
MMP1497 hypothetical protein MMP1497 27, 77
MMP1498 hypothetical protein MMP1498 27, 77
MMP1510 gatA aspartyl/glutamyl-tRNA amidotransferase subunit A 27, 77
MMP1512 alr alanine racemase 8, 21
MMP1513 ald alanine dehydrogenase 8, 21
MMP1515 hsp60 chaperonin GroEL 77, 96
MMP1527 aspartate aminotransferase 8, 21
MMP1531 hypothetical protein MMP1531 8, 66
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
MMP1592 trpS tryptophanyl-tRNA synthetase 27, 143
MMP1593 hypothetical protein MMP1593 27, 77
MMP1615 hypothetical protein MMP1615 7, 112
MMP1656 glutamine amidotransferase subunit PdxT 8, 137
MMP1698 hypothetical protein MMP1698 4, 8
MMP1699 hypothetical protein MMP1699 77, 136
MMP1701 amino acid-binding ACT domain-containing protein 27, 40
MMP1702 hom homoserine dehydrogenase 27, 40
MMP1705 creatininase 8, 11, 20
Unanno_15 None 8, 44
Unanno_17 None 8, 126
Unanno_19 None 77, 138
Unanno_8 None 8, 78
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
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Comments for MMP1588
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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