Organism : Methanococcus maripaludis S2 | Module List :
MMP0218

hypothetical protein MMP0218

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0218
(Mouseover regulator name to see its description)

MMP0218 is regulated by 17 influences and regulates 0 modules.
Regulators for MMP0218 (17)
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
MMP0032
MMP0907
104 combiner
MMP0097
MMP1467
104 combiner
MMP0031
H2
15 combiner
MMP0480
H2
15 combiner
MMP0480
MMP1210
15 combiner
MMP1303 15 tf

Warning: MMP0218 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
691 1.40e+01 ggtTGAaAAtaTCgTAAtTT
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692 2.90e+01 cTGcgGTg
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765 2.20e+01 AtctgTaAgtTT.gAggtAaaacC
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766 7.80e+01 acACcggaAataTTgTTccaaGC
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865 3.00e+02 tgtAAc.gttccTGg
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866 3.10e+03 cCCCCG
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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 MMP0218

Warning: No Functional annotations were found!

Module neighborhood information for MMP0218

MMP0218 has total of 82 gene neighbors in modules 15, 52, 104
Gene neighbors (82)
Gene Common Name Description Module membership
Antisense_1 None 85, 104
Antisense_6 None 52, 67
MMP0011 DNA-cytosine methyltransferase 4, 104
MMP0013 argH argininosuccinate lyase 52, 120
MMP0019 hypothetical protein MMP0019 14, 104, 142
MMP0025 hypothetical protein MMP0025 8, 52
MMP0077 radical SAM domain-containing protein 35, 104
MMP0125 flpA fibrillarin-like protein 14, 104
MMP0126 bioB biotin synthase 14, 104
MMP0161 comB 2-phosphosulfolactate phosphatase 85, 104
MMP0170 cofF RimK family alpha-L-glutamate ligase 104, 133
MMP0186 hypothetical protein MMP0186 104, 133
MMP0202 permease 52, 67
MMP0203 hypothetical protein MMP0203 52, 67
MMP0214 putative deoxyribonucleotide triphosphate pyrophosphatase 12, 104
MMP0218 hypothetical protein MMP0218 15, 52, 104
MMP0227 nrdD anaerobic ribonucleoside-triphosphate reductase 15, 67
MMP0236 hypothetical protein MMP0236 75, 104
MMP0252 hypothetical protein MMP0252 15, 46
MMP0262 hypothetical protein MMP0262 52, 67
MMP0328 hypothetical protein MMP0328 15, 157
MMP0349 2-hydroxyglutaryl-CoA dehydratase subunit A-like protein 15, 80
MMP0355 hypothetical protein MMP0355 52, 78
MMP0362 hypothetical protein MMP0362 15, 163
MMP0363 methanol dehydrogenase regulatory protein-like protein 15, 46
MMP0366 hypothetical protein MMP0366 15, 163
MMP0367 hypothetical protein MMP0367 15, 163
MMP0374 hypothetical protein MMP0374 15, 46
MMP0376 ATP dependent DNA ligase 15, 52
MMP0377 isoleucyl-tRNA synthetase-like protein 52, 78
MMP0378 amidohydrolase 15, 52
MMP0379 hypothetical protein MMP0379 104, 163
MMP0380 dnaB DNA polymerase family B protein 15, 104
MMP0390 hypothetical protein MMP0390 15, 157
MMP0392 purD phosphoribosylamine--glycine ligase 4, 75, 104
MMP0394 hemD uroporphyrinogen III synthase 15, 46
MMP0395 hypothetical protein MMP0395 15, 46
MMP0401 metE methionine synthase 4, 15, 80
MMP0402 hypothetical protein MMP0402 15, 70
MMP0409 glucose-methanol-choline oxidoreductase 15, 52
MMP0410 prsA ribose-phosphate pyrophosphokinase 52, 78
MMP0411 comD sulfopyruvate decarboxylase subunit alpha 15, 46
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
MMP0561 cmd carboxymuconolactone decarboxylase 52, 111
MMP0617 radB DNA repair and recombination protein RadB 52, 67
MMP0655 hypothetical protein MMP0655 24, 38, 52
MMP0731 exodeoxyribonuclease VII small subunit 85, 104
MMP0811 hypothetical protein MMP0811 52, 67
MMP0895 hypothetical protein MMP0895 14, 104
MMP0909 hypothetical protein MMP0909 75, 104
MMP0986 thyA thymidylate synthase 104, 142
MMP1027 hypothetical protein MMP1027 104, 163
MMP1070 hypothetical protein MMP1070 8, 15
MMP1093 coaD phosphopantetheine adenylyltransferase 52, 70
MMP1117 hypothetical protein MMP1117 14, 47, 52, 139
MMP1120 ATPase-like ATP-binding protein 52, 67
MMP1166 iron-sulfur flavoprotein 15, 90
MMP1167 flavoprotein-like protein 15, 90
MMP1168 ABC transporter ATP-binding protein 15, 46
MMP1169 SufBD protein 15, 46
MMP1202 hypothetical protein MMP1202 104, 153
MMP1203 cbiD cobalt-precorrin-6A synthase 104, 153
MMP1204 M24 family metallopeptidase 15, 68
MMP1232 PP-loop domain-containing protein 95, 104
MMP1253 hypothetical protein MMP1253 52, 120
MMP1264 hypothetical protein MMP1264 104, 142, 157
MMP1312 hypothetical protein MMP1312 52, 140
MMP1313 fen-1 flap endonuclease-1 47, 52, 141
MMP1314 phosphoesterase domain-containing protein 52, 120
MMP1350 radical SAM domain-containing protein 14, 47, 104
MMP1377 hypothetical protein MMP1377 69, 104
MMP1485 moaB molybdenum cofactor biosynthesis protein 104, 142
MMP1494 hypothetical protein MMP1494 104, 153
MMP1554 hypothetical protein MMP1554 15, 139
MMP1600 ribosomal protein S6 modification protein 104, 129
MMP1648 hypothetical protein MMP1648 14, 47, 52, 139
Unanno_14 None 52, 67
Unanno_33 None 52, 78
Unanno_59 None 28, 104, 133
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 MMP0218
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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