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 12664 to 12713 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
1081 secretory carrier-associated membrane protein 3. [swissprot;acc:o14828] Measured Divided 6439.3 7031.73 1.092
1082 atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542] Rooted 61.6272 64.6988 1.04984
calcium-transporting atpase type 2c, member 1 (ec 3.6.3.8) (atpase 2c1) (atp-dependent ca(2+) pump pmr1) (hussy-28). [swissprot;acc:p98194] Ranked Subtracted 209.052 203.183 5.869
cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569] Rooted 63.2689 66.4479 3.179
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Measured 5364.77 5884.89 520.12
hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839] Squared Divided 21803 24991 1.14622
phafin 2; ph and fyve domain-containing protein 2. [refseq;acc:nm_024613] Ranked 220.118 213.685 1.03011
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] Squared Subtracted 20131.3 23416.5 3285.2
secretory carrier-associated membrane protein 1. [swissprot;acc:o15126] Measured Divided 6439.35 7031.8 1.092
1083 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Ranked 220.118 213.685 1.03011
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6] Subtracted 217.99 212.123 5.867
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047] Rooted Divided 61.6272 64.6988 1.04984
exocyst complex component sec15b. [swissprot;acc:q9y2d4] Measured 6213.51 6785.04 1.09198
hect type e3 ubiquitin ligase. [refseq;acc:nm_015052] Rooted Subtracted 63.2689 66.4479 3.179
hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219] Squared Divided 21803 24991 1.14622
phosphomannomutase 2 (ec 5.4.2.8) (pmm 2). [swissprot;acc:o15305] Measured Subtracted 5511.96 6031.95 519.99
sr rich protein. [refseq;acc:nm_032870] Squared 35530.1 32245.4 3284.7
1084 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Ranked Divided 220.118 213.685 1.03011
adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566] Measured Subtracted 7444.28 7964 519.72
alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] Squared 29470.8 32748.2 3277.4
argininosuccinate synthase (ec 6.3.4.5) (citrulline--aspartate ligase). [swissprot;acc:p00966] Divided 24976.9 28625.4 1.14607
phosphatidate cytidylyltransferase 2 (ec 2.7.7.41) (cdp-diglyceride synthetase 2) (cdp-diglyceride pyrophosphorylase 2) (cdp- diacylglycerol synthase 2) (cds 2) (ctp:phosphatidate cytidylyltransferase 2) (cdp-dag synthase 2) (cdp-dg synthetase 2). [swissprot;acc:o95674] Measured 6437.49 7029.22 1.09192
transducin-like enhancer protein 3 (esg3). [swissprot;acc:q04726] Rooted Subtracted 63.2671 66.4459 3.1788
translocon-associated protein, delta subunit precursor (trap-delta) (signal sequence receptor delta subunit) (ssr-delta). [swissprot;acc:p51571] Divided 82.1841 86.2754 1.04978
vacuolar proton translocating atpase 116 kda subunit a isoform 1 (clathrin-coated vesicle/synaptic vesicle proton pump 116 kda subunit) (vacuolar proton pump subunit 1) (vacuolar adenosine triphosphatase subunit ac116). [swissprot;acc:q93050] Ranked Subtracted 218.529 212.676 5.853
1085 calsyntenin-1 precursor. [swissprot;acc:o94985] Rooted Divided 82.1841 86.2754 1.04978
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Ranked 231.007 237.864 1.02968
gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Rooted Subtracted 71.8595 75.0311 3.1716
glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057] Measured Divided 6520.28 7119.28 1.09187
myb-related protein b (b-myb). [swissprot;acc:p10244] Squared Subtracted 22817.9 26093.4 3275.5
peroxiredoxin 4 (ec 1.11.1.-) (prx-iv) (thioredoxin peroxidase ao372) (thioredoxin-dependent peroxide reductase a0372) (antioxidant enzyme aoe372) (aoe37-2). [swissprot;acc:q13162] Measured 6343.26 6862.94 519.68
transcription factor smif; decapping enzyme hdcp1a. [refseq;acc:nm_018403] Squared Divided 21394.9 24518.9 1.14602
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Ranked Subtracted 218.528 212.676 5.852
1086 atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]
caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844] Squared Divided 19918.7 22827.3 1.14602
dimethylaniline monooxygenase [n-oxide forming] 2 (ec 1.14.13.8) (pulmonary flavin-containing monooxygenase 2) (fmo 2) (dimethylaniline oxidase 2) (fmo 1b1). [swissprot;acc:q99518] Measured Subtracted 5365.06 5884.52 519.46
estradiol 17 beta-dehydrogenase 4 (ec 1.1.1.62) (17-beta-hsd 4) (17-beta-hydroxysteroid dehydrogenase 4). [swissprot;acc:p51659] Squared 26751.5 30026.4 3274.9
exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Rooted 58.8768 62.0483 3.1715
proline oxidase, mitochondrial precursor (ec 1.5.3.-) (proline dehydrogenase). [swissprot;acc:o43272] Measured Divided 6520.28 7119.28 1.09187
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Ranked 236.679 243.679 1.02958
succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521] Rooted 82.1841 86.2754 1.04978
1087 aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] Squared Subtracted 25544.9 28816.9 3272
junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Measured Divided 5732.73 6256.63 1.09139
protein-tyrosine phosphatase beta precursor (ec 3.1.3.48) (r-ptp- beta). [swissprot;acc:p23467] Rooted 82.184 86.2753 1.04978
suppressor of var1, 3-like 1. [refseq;acc:nm_003171] Measured Subtracted 6439.79 6959.21 519.42
transducin-like enhancer protein 4. [swissprot;acc:q04727] Rooted 63.2297 66.4011 3.1714
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Ranked 218.527 212.676 5.851
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Squared Divided 19479.8 22320.6 1.14583
zinc finger protein 277. [swissprot;acc:q9nrm2] Ranked 236.679 243.679 1.02958
1088 annexin a11 (annexin xi) (calcyclin-associated annexin 50) (cap-50) (56 kda autoantigen). [swissprot;acc:p50995] 219.673 213.378 1.0295

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/