Organism : Methanococcus maripaludis S2 | Module List :
MMP0081 gltB

glutamate synthase large subunit

CircVis
Functional Annotations (10)
Function System
Glutamate synthase domain 2 cog/ cog
dihydroorotate dehydrogenase activity go/ molecular_function
glutamate synthase (NADPH) activity go/ molecular_function
electron transport go/ biological_process
'de novo' pyrimidine base biosynthetic process go/ biological_process
glutamate biosynthetic process go/ biological_process
electron carrier activity go/ molecular_function
glutamate synthase complex (NADPH) go/ cellular_component
glutamate synthase (NADH) activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0081
(Mouseover regulator name to see its description)

MMP0081 is regulated by 15 influences and regulates 0 modules.
Regulators for MMP0081 gltB (15)
Regulator Module Operator
MMP0033
H2
60 combiner
MMP0052 60 tf
MMP0907
MMP1646
60 combiner
MMP1015 60 tf
MMP1303
MMP1646
60 combiner
H2 112 ef
MMP0052 112 tf
MMP0637 112 tf
MMP0907
MMP1646
112 combiner
MMP1467
MMP1646
112 combiner
MMP0052 16 tf
MMP0052
MMP0480
16 combiner
MMP0460 16 tf
MMP1015 16 tf
MMP1467
MMP1646
16 combiner

Warning: MMP0081 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
693 2.50e+01 AcGGTG
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694 1.30e+03 GGTTcCAGAAtCCC
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781 1.80e+03 cGaATTtaCgG
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782 2.90e+03 CTCGCACC
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881 4.20e+02 TGGTT.CAgaAtCCC
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882 3.70e+02 AAtgggGcgagaac
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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 MMP0081

MMP0081 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Glutamate synthase domain 2 cog/ cog
dihydroorotate dehydrogenase activity go/ molecular_function
glutamate synthase (NADPH) activity go/ molecular_function
electron transport go/ biological_process
'de novo' pyrimidine base biosynthetic process go/ biological_process
glutamate biosynthetic process go/ biological_process
electron carrier activity go/ molecular_function
glutamate synthase complex (NADPH) go/ cellular_component
glutamate synthase (NADH) activity go/ molecular_function
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for MMP0081

MMP0081 has total of 40 gene neighbors in modules 16, 60, 112
Gene neighbors (40)
Gene Common Name Description Module membership
MMP0080 glutamate synthase large subunit 7, 60
MMP0081 gltB glutamate synthase large subunit 16, 60, 112
MMP0082 glutamate synthase large subunit 16, 112
MMP0083 coenzyme F420 hydrogenase/dehydrogenase subunit beta domain-containing protein 16, 112
MMP0162 hypothetical protein MMP0162 16, 112
MMP0163 arsA arsenite-activated ATPase ArsA 16, 96
MMP0224 hemL glutamate-1-semialdehyde aminotransferase 60, 130, 140
MMP0297 aIF-2_beta translation initiation factor IF-2 subunit beta 60, 81
MMP0414 thrS threonyl-tRNA synthetase 8, 81, 112
MMP0417 hisA 1-(5-phosphoribosyl)-5- 60, 137
MMP0418 carbohydrate kinase PfkB 60, 137, 143
MMP0540 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 8, 112, 143
MMP0597 flpA fibrillarin 8, 16, 81
MMP0639 50S ribosomal protein L24e 16, 92, 130
MMP0640 rps28e 30S ribosomal protein S28e 16, 92, 130
MMP0641 rpl7ae 50S ribosomal protein L7Ae 16, 92, 130
MMP0696 proS prolyl-tRNA synthetase 7, 60
MMP0704 ParA type ATPase 8, 78, 112
MMP0880 aksF isopropylmalate/isohomocitrate dehydrogenase 24, 60, 140, 143
MMP0893 pyrG CTP synthetase 7, 60
MMP0894 guaA GMP synthase subunit B 60, 112
MMP0955 sucD succinyl-CoA synthetase subunit alpha 60, 120
MMP1017 lysC aspartate kinase 24, 60, 112
MMP1146 purF amidophosphoribosyltransferase 7, 60, 137, 143
MMP1148 small nuclear ribonucleoprotein 16, 63
MMP1188 hypothetical protein MMP1188 60, 112
MMP1189 ribose-5-phosphate isomerase A 60, 139
MMP1255 pheT phenylalanyl-tRNA synthetase subunit beta 60, 120
MMP1306 hypothetical protein MMP1306 16, 112
MMP1308 tal putative translaldolase 8, 16, 112
MMP1426 dcd bifunctional dCTP deaminase/dUTP diphosphatase 16, 112, 140
MMP1427 hypothetical protein MMP1427 81, 112
MMP1437 top6A DNA topoisomerase VI subunit A 39, 112
MMP1474 ileS isoleucyl-tRNA synthetase 16, 20
MMP1480 aconitase family 60, 87, 92
MMP1583 S-adenosylmethionine decarboxylase-like protein 21, 112
MMP1585 arginase 41, 112
MMP1615 hypothetical protein MMP1615 7, 112
MMP1616 aspC aspartyl-tRNA synthetase 16, 112
MMP1640 S-adenosylmethionine synthetase 16, 60
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 MMP0081
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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