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 2713 to 2762 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
1357 dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2] Divided 5657.71 6103.54 1.0788
flotillin-1. [swissprot;acc:o75955] Subtracted 5655.85 6120.64 464.79
1358 sestrin 1 (p53-regulated protein pa26). [swissprot;acc:q9y6p5] 6120.62 464.77
zinc finger protein zic 4 (zinc finger protein of the cerebellum 4) (fragment). [swissprot;acc:q8n9l1] Divided 5657.71 6103.54 1.0788
1359 dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]
isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] Subtracted 5779.83 6244.56 464.73
1360 calcipressin 2 (thyroid hormone-responsive protein zaki-4) (down syndrome candidate region 1-like 1) (myocyte-enriched calcineurin interacting protein 2) (mcip2). [swissprot;acc:q14206] Divided 5657.72 6103.52 1.07879
vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459] Subtracted 6192.38 6656.34 463.96
1361 calcipressin 3 (down syndrome candidate region 1-like protein 2) (myocyte-enriched calcineurin interacting protein 3) (mcip3). [swissprot;acc:q9uka8] Divided 5657.72 6103.52 1.07879
u2 small nuclear ribonucleoprotein b". [swissprot;acc:p08579] Subtracted 5675.96 6136.47 460.51
1362 deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366] 6146.36 6606.21 459.85
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Divided 6322.75 6820.5 1.07872
1363 nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307]
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Subtracted 6343.76 6803.44 459.68
1364 dna polymerase gamma subunit 1 (ec 2.7.7.7) (mitochondrial dna polymerase catalytic subunit) (polg-alpha). [swissprot;acc:p54098] 5685.77 6145.43 459.66
protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] Divided 5815.14 6272.66 1.07868
1365 cytochrome oxidase biogenesis protein oxa1, mitochondrial precursor (oxa1-like protein) (oxa1hs). [swissprot;acc:q15070] Subtracted 5589.33 6047.9 458.57
gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Divided 5799.14 6255.04 1.07862
1366 60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48] Subtracted 5589.33 6047.9 458.57
megf11 protein. [refseq;acc:nm_032445] Divided 5793.55 6248.79 1.07858
1367 hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Subtracted 6152.78 6610.46 457.68
megf10 protein. [refseq;acc:nm_032446] Divided 5793.47 6248.71 1.07858
1368 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Subtracted 6152.78 6610.46 457.68
beta adducin (erythrocyte adducin beta subunit). [swissprot;acc:p35612] Divided 5793.29 6248.51 1.07858
1369 alpha adducin (erythrocyte adducin alpha subunit). [swissprot;acc:p35611] 5786.71 6241.16 1.07853
guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Subtracted 6152.78 6610.46 457.68
1370 protein c20orf4 (protein cgi-23) (pro0225). [swissprot;acc:q9y312] 5815.14 6272.66 457.52
t-complex associated-testis-expressed 1-like (protein 91/23). [swissprot;acc:p51808] Divided 10231.8 9487.34 1.07847
1371 double-strand break repair protein mre11a (mre11 homolog 1). [swissprot;acc:p49959]
glycogenin-1 (ec 2.4.1.186). [swissprot;acc:p46976] Subtracted 6376.12 6833.59 457.47
1372 adenosine kinase (ec 2.7.1.20) (ak) (adenosine 5'-phosphotransferase). [swissprot;acc:p55263]
lin-7 homolog a; vertebrate lin7 homolog 1; tax interaction protein 33; mammalian lin-7 1. [refseq;acc:nm_004664] Divided 5743.45 6193.45 1.07835
1373 mitogen-activated protein kinase 3 (ec 2.7.1.37) (extracellular signal-regulated kinase 1) (erk-1) (insulin-stimulated map2 kinase) (map kinase 1) (mapk 1) (p44-erk1) (ert2) (p44-mapk) (microtubule- associated protein-2 kinase). [swissprot;acc:p27361] 6079.85 6556.07 1.07833
protein x 0001. [refseq;acc:nm_016302] Subtracted 6376.12 6833.59 457.47
1374 glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]
ribosomal protein s6 kinase alpha 3 (ec 2.7.1.37) (s6k-alpha 3) (90 kda ribosomal protein s6 kinase 3) (p90-rsk 3) (ribosomal s6 kinase 2) (rsk-2) (pp90rsk2) (insulin-stimulated protein kinase 1) (ispk-1). [swissprot;acc:p51812] Divided 6079.45 6555.4 1.07829
1375 calcium/calmodulin-dependent protein kinase type ii gamma chain (ec 2.7.1.123) (cam-kinase ii gamma chain) (cam kinase ii gamma subunit) (camk-ii gamma subunit) (fragment). [swissprot;acc:q13555]
mitotic checkpoint serine/threonine-protein kinase bub1 beta (ec 2.7.1.-) (hbubr1) (mad3/bub1-related protein kinase) (mitotic checkpoint kinase mad3l). [swissprot;acc:o60566] Subtracted 5528.65 5985.58 456.93
1376 calcium/calmodulin-dependent protein kinase type ii delta chain (ec 2.7.1.123) (cam-kinase ii delta chain) (cam kinase ii delta subunit) (camk-ii delta subunit). [swissprot;acc:q13557] Divided 6079.46 6555.41 1.07829
pyridoxine 5'-phosphate oxidase. [refseq;acc:nm_018129] Subtracted 5528.65 5985.58 456.93
1377 mitogen-activated protein kinase kinase kinase 6 (ec 2.7.1.-). [swissprot;acc:o95382] Divided 6079.46 6555.4 1.07829
transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. [swissprot;acc:p55072] Subtracted 6449.02 6905.56 456.54
1378 ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [swissprot;acc:p00480] 5783.9 6240.19 456.29
signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556] Divided 6079.45 6555.4 1.07829
1379 gamma adducin (adducin-like protein 70). [swissprot;acc:q9uey8] Subtracted 5799.14 6255.04 455.9
ribosomal protein s6 kinase alpha 1 (ec 2.7.1.37) (s6k-alpha 1) (90 kda ribosomal protein s6 kinase 1) (p90-rsk 1) (ribosomal s6 kinase 1) (rsk-1) (pp90rsk1). [swissprot;acc:q15418] Divided 6079.46 6555.41 1.07829
1380 atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288]
fuse-binding protein-interacting repressor isoform b; siah binding protein 1; pyrimidine tract binding splicing factor; ro ribonucleoprotein-binding protein 1; poly-u binding splicing factor puf60. [refseq;acc:nm_014281] Subtracted 6364.01 6819.38 455.37
1381 glutaryl-coa dehydrogenase, mitochondrial precursor (ec 1.3.99.7) (gcd). [swissprot;acc:q92947] Divided 6079.46 6555.41 1.07829
multisynthetase complex auxiliary component p38 (jtv-1 protein) (pro0992). [swissprot;acc:q13155] Subtracted 6364.01 6819.38 455.37

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/