Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 12214 to 12263 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1025 nadph:adrenodoxin oxidoreductase, mitochondrial precursor (ec 1.18.1.2) (adrenodoxin reductase) (ar) (ferredoxin-nadp(+) reductase). [swissprot;acc:p22570] Measured Subtracted 5947.53 6481.56 534.03
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Squared 21095.7 24507.5 3411.8
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Measured Divided 5511.96 6031.95 1.09434
1026 apopain precursor (ec 3.4.22.-) (cysteine protease cpp32) (yama protein) (cpp-32) (caspase-3) (casp-3) (srebp cleavage activity 1) (sca-1). [swissprot;acc:p42574] Rooted 55.3631 58.2965 1.05298
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] Ranked Subtracted 231.922 238.486 6.564
inorganic pyrophosphatase 2 isoform 1. [refseq;acc:nm_176869] Squared Divided 22126.7 25398.5 1.14787
limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449] Measured Subtracted 5396.36 5929.41 533.05
phosphomannomutase 1 (ec 5.4.2.8) (pmm 1) (pmmh-22). [swissprot;acc:q92871] Divided 5509.89 6029.29 1.09427
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Rooted Subtracted 54.765 51.4319 3.3331
transforming protein rhoa (h12). [swissprot;acc:p06749] Ranked Divided 205.632 199.266 1.03195
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Squared Subtracted 19970 23366.8 3396.8
1027 adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Ranked 211.449 217.998 6.549
aryl-hydrocarbon interacting protein-like 1. [swissprot;acc:q9nzn9] Squared Divided 22126.7 25398.5 1.14787
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Rooted Subtracted 54.765 51.4319 3.3331
cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] Divided 52.1219 49.5013 1.05294
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982] Measured Subtracted 5406.5 5939.42 532.92
s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] Divided 6123.15 6700.05 1.09422
succinyl-coa ligase [gdp-forming] alpha-chain, mitochondrial precursor (ec 6.2.1.4) (succinyl-coa synthetase, alpha chain) (scs-alpha). [swissprot;acc:p53597] Ranked 211.908 218.627 1.03171
tetratricopeptide repeat protein 4 (my044 protein). [swissprot;acc:o95801] Squared Subtracted 30900.2 34294.9 3394.7
1028 ah receptor-interacting protein (aip) (immunophilin homolog ara9) (hbv-x associated protein 2). [swissprot;acc:o00170] Divided 22126.7 25398.5 1.14787
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Ranked Subtracted 211.449 217.998 6.549
glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695] Squared 23321.3 26715.4 3394.1
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Rooted 54.765 51.4319 3.3331
neurotrimin precursor (hnt). [swissprot;acc:q9p121] Measured 5413.63 5946.46 532.83
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [swissprot;acc:q15274] Divided 5704 6241.36 1.09421
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1] Rooted 52.1219 49.5013 1.05294
succinyl-coa ligase [adp-forming] beta-chain, mitochondrial precursor (ec 6.2.1.5) (succinyl-coa synthetase, betaa chain) (scs-betaa) (atp- specific succinyl-coa synthetase beta subunit). [swissprot;acc:q9p2r7] Ranked 211.908 218.627 1.03171
1029 17 beta-hydroxysteroid dehydrogenase. [sptrembl;acc:q13034] Subtracted 211.449 217.998 6.549
beta-catenin (pro2286). [swissprot;acc:p35222] Measured Divided 5635.26 6166.09 1.0942
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Rooted Subtracted 54.765 51.4319 3.3331
dna damage binding protein 1 (damage-specific dna binding protein 1) (ddb p127 subunit) (ddba) (uv-damaged dna-binding protein 1) (uv-ddb 1) (xeroderma pigmentosum group e complementing protein) (xpce) (x- associated protein 1) (xap-1). [swissprot;acc:q16531] Ranked Divided 222.364 215.535 1.03168
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Squared 31999.3 36726.8 1.14774
ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [swissprot;acc:p50053] Subtracted 22569.9 25956.6 3386.7
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999] Measured 4726.38 5258.95 532.57
senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493] Rooted Divided 52.1219 49.5013 1.05294
1030 casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674] Measured 5048.33 5523.85 1.09419
electron transfer flavoprotein alpha-subunit, mitochondrial precursor (alpha-etf). [swissprot;acc:p13804] Subtracted 7919.76 8452.01 532.25
mitochondrial ferritin; ferritin heavy chain-like; ferritin h subunit. [refseq;acc:nm_177478] Squared Divided 31994.3 36720 1.1477
oligophrenin 1. [swissprot;acc:o60890] Rooted 52.1219 49.5013 1.05294
propionyl-coa carboxylase beta chain, mitochondrial precursor (ec 6.4.1.3) (pccase beta subunit) (propanoyl-coa:carbon dioxide ligase beta subunit). [swissprot;acc:p05166] Ranked 222.364 215.535 1.03168
purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [swissprot;acc:p00491] Squared Subtracted 22569.9 25956.6 3386.7
retinol dehydrogenase 8 (all-trans); photoreceptor outer segment all-trans retinol dehydrogenase. [refseq;acc:nm_015725] Ranked 211.449 217.998 6.549
ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Rooted 70.4902 73.8211 3.3309
1031 cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836] Squared Divided 31994 36719.6 1.1477
hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Ranked Subtracted 219.01 212.468 6.542
kappa b-ras 1. [refseq;acc:nm_020345] Rooted Divided 61.2289 64.4564 1.05271
membrane protein expressed in epithelial-like lung adenocarcinoma. [refseq;acc:nm_024792] Measured 6136.99 6714.98 1.09418
peroxisomal membrane protein 2 (22 kda peroxisomal membrane protein). [swissprot;acc:q9nr77] Subtracted 6437.99 6969.67 531.68
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Squared 26925.7 30311.3 3385.6
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Ranked Divided 242.978 235.518 1.03167

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/