Organism : Methanococcus maripaludis S2 | Module List :
MMP1117

hypothetical protein MMP1117

CircVis
Functional Annotations (1)
Function System
Predicted Fe-S-cluster oxidoreductase cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1117
(Mouseover regulator name to see its description)

MMP1117 is regulated by 28 influences and regulates 0 modules.
Regulators for MMP1117 (28)
Regulator Module Operator
MMP0031
H2
52 combiner
MMP0086
MMP1023
52 combiner
MMP0402 52 tf
MMP0465 52 tf
MMP1023
MMP1210
52 combiner
MMP1052 52 tf
MMP1052
Formate
52 combiner
MMP1303 52 tf
MMP1304 52 tf
MMP1447 52 tf
MMP1499 52 tf
MMP0033 47 tf
MMP0033
MMP0629
47 combiner
MMP0629
MMP1499
47 combiner
MMP0907
MMP1023
47 combiner
MMP1704 47 tf
MMP0031
MMP0637
14 combiner
MMP0033 14 tf
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: MMP1117 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
689 7.10e+00 TGGtgGt
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690 2.90e+04 GGtGGcAC
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755 3.90e+02 TaA.TTaTccGgaAATTaCc
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756 4.00e+03 CCCCtCC
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765 2.20e+01 AtctgTaAgtTT.gAggtAaaacC
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766 7.80e+01 acACcggaAataTTgTTccaaGC
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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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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 MMP1117

MMP1117 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Predicted Fe-S-cluster oxidoreductase cog/ cog
Module neighborhood information for MMP1117

MMP1117 has total of 89 gene neighbors in modules 14, 47, 52, 139
Gene neighbors (89)
Gene Common Name Description Module membership
Antisense_6 None 52, 67
MMP0013 argH argininosuccinate lyase 52, 120
MMP0019 hypothetical protein MMP0019 14, 104, 142
MMP0021 hypothetical protein MMP0021 14, 142
MMP0025 hypothetical protein MMP0025 8, 52
MMP0056 cofH FO synthase subunit 2 14, 139
MMP0099 major facilitator transporter 14, 92
MMP0124 membrane-bound metal-dependent hydrolase 14, 67
MMP0125 flpA fibrillarin-like protein 14, 104
MMP0126 bioB biotin synthase 14, 104
MMP0152 citrate transporter 14, 139
MMP0202 permease 52, 67
MMP0203 hypothetical protein MMP0203 52, 67
MMP0218 hypothetical protein MMP0218 15, 52, 104
MMP0222 hypothetical protein MMP0222 14, 122, 157
MMP0262 hypothetical protein MMP0262 52, 67
MMP0291 hydrogenase expression/formation protein-like protein 47, 122
MMP0320 shikimate kinase 47, 141
MMP0353 UDP-glucose/GDP-mannose dehydrogenase-like protein 80, 139
MMP0355 hypothetical protein MMP0355 52, 78
MMP0356 group 1 glycosyl transferase 80, 139, 140
MMP0357 UDP-N-acetylglucosamine 2-epimerase 139, 157
MMP0358 hypothetical protein MMP0358 139, 157
MMP0376 ATP dependent DNA ligase 15, 52
MMP0377 isoleucyl-tRNA synthetase-like protein 52, 78
MMP0378 amidohydrolase 15, 52
MMP0409 glucose-methanol-choline oxidoreductase 15, 52
MMP0410 prsA ribose-phosphate pyrophosphokinase 52, 78
MMP0415 O-sialoglycoprotein endopeptidase/protein kinase 47, 149
MMP0428 vanadium nitrogenase-associated-like protein N 14, 68
MMP0446 nitrogen fixation-like protein 52, 67
MMP0488 low molecular weight phosphotyrosine protein phosphatase 52, 67
MMP0489 hypothetical protein MMP0489 52, 67
MMP0498 hypothetical protein MMP0498 52, 70
MMP0541 serB phosphoserine phosphatase SerB 7, 40, 139, 140
MMP0561 cmd carboxymuconolactone decarboxylase 52, 111
MMP0579 hypothetical protein MMP0579 115, 139
MMP0582 AzlC family protein 47, 68
MMP0617 radB DNA repair and recombination protein RadB 52, 67
MMP0655 hypothetical protein MMP0655 24, 38, 52
MMP0681 xanthine/uracil permease family protein 47, 162
MMP0713 iorA2 indolepyruvate oxidoreductase subunit alpha 2 24, 47, 86
MMP0714 iorB2 indolepyruvate oxidoreductase subunit beta 24, 47, 86
MMP0811 hypothetical protein MMP0811 52, 67
MMP0895 hypothetical protein MMP0895 14, 104
MMP0905 hypothetical protein MMP0905 14, 149
MMP0907 transcriptional regulator TrmB 14, 149
MMP0938 cobS cobalamin (5'-phosphate) synthase 47, 122
MMP0970 lig DNA ligase I, ATP-dependent Dnl1 47, 129
MMP0989 top6B DNA topoisomerase VI subunit B 139, 141
MMP1024 MCE family-like protein 14, 47, 157
MMP1048 hypothetical protein MMP1048 14, 25
MMP1077 phosphoglucomutase/phosphomannomutase 40, 68, 139
MMP1080 group 1 glycosyl transferase 14, 142
MMP1089 polysaccharide biosynthesis protein 14, 70
MMP1093 coaD phosphopantetheine adenylyltransferase 52, 70
MMP1103 hypothetical protein MMP1103 14, 38
MMP1117 hypothetical protein MMP1117 14, 47, 52, 139
MMP1120 ATPase-like ATP-binding protein 52, 67
MMP1128 ppiB cyclophilin type peptidyl-prolyl cis-trans isomerase 47, 86
MMP1143 hypothetical protein MMP1143 14, 47
MMP1175 hypothetical protein MMP1175 14, 136
MMP1189 ribose-5-phosphate isomerase A 60, 139
MMP1253 hypothetical protein MMP1253 52, 120
MMP1262 hypothetical protein MMP1262 14, 151
MMP1287 hypothetical protein MMP1287 14, 47, 80
MMP1288 UbiD family decarboxylase 47, 80
MMP1312 hypothetical protein MMP1312 52, 140
MMP1313 fen-1 flap endonuclease-1 47, 52, 141
MMP1314 phosphoesterase domain-containing protein 52, 120
MMP1327 rpoK RNA polymerase Rpb6 103, 139, 149
MMP1328 enolase 103, 139, 149
MMP1348 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase 14, 47
MMP1350 radical SAM domain-containing protein 14, 47, 104
MMP1356 PP-loop domain-containing protein 25, 129, 139, 140, 149
MMP1373 purP 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase 14, 35
MMP1438 hypothetical protein MMP1438 14, 140
MMP1491 trzA amidohydrolase 14, 111, 122, 149
MMP1492 pyrE orotate phosphoribosyltransferase 14, 149
MMP1499 hypothetical protein MMP1499 14, 139
MMP1500 ftsz2 cell division protein FtsZ 139, 157
MMP1521 hypothetical protein MMP1521 14, 111, 122, 157
MMP1554 hypothetical protein MMP1554 15, 139
MMP1587 hypothetical protein MMP1587 7, 14, 80
MMP1610 hypothetical protein MMP1610 19, 139
MMP1648 hypothetical protein MMP1648 14, 47, 52, 139
MMP1711 pcnA proliferating cell nuclear antigen 115, 139
Unanno_14 None 52, 67
Unanno_33 None 52, 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
  • 6. Visualisation legend
Comments for MMP1117
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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