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 6762 to 6811 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1691 ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Rooted 49.7922 48.1871 1.03331
translation initiation factor if-2. [swissprot;acc:o60841] Ranked 217.263 214.315 1.01376
upf0183 protein. [swissprot;acc:q9bsu1] Measured 5767.69 6165.87 1.06904
1692 antithrombin-iii precursor (atiii) (pro0309). [swissprot;acc:p01008]
proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072] Rooted 64.1296 66.2619 1.03325
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] Squared 13040.7 14416.9 1.10553
rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251] Ranked 218.515 215.551 1.01375
1693 c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319] Rooted 62.1092 64.1674 1.03314
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] Squared 9190.5 10160.2 1.10551
inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268] Ranked 218.937 215.971 1.01373
translation initiation factor eif-2b alpha subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q14232] Measured 5767.69 6165.87 1.06904
1694 gmp synthase [glutamine-hydrolyzing] (ec 6.3.5.2) (glutamine amidotransferase) (gmp synthetase). [swissprot;acc:p49915] Ranked 218.937 215.971 1.01373
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475] Squared 26226.9 28993.4 1.10548
squamous cell carcinoma antigen 1 (scca-1) (protein t4-a). [swissprot;acc:p29508] Measured 5767.69 6165.87 1.06904
tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748] Rooted 62.1123 64.1674 1.03309
1695 inosine-5'-monophosphate dehydrogenase 1 (ec 1.1.1.205) (imp dehydrogenase 1) (impdh-i) (impd 1). [swissprot;acc:p20839] Ranked 218.937 215.971 1.01373
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [swissprot;acc:q13133] Measured 5767.69 6165.87 1.06904
peroxisomal membrane protein pex14 (peroxin-14) (peroxisomal membrane anchor protein pex14) (pts1 receptor docking protein). [swissprot;acc:o75381] Squared 29823.4 32961.5 1.10522
proteasome subunit beta type 3 (ec 3.4.25.1) (proteasome theta chain) (proteasome chain 13) (proteasome component c10-ii). [swissprot;acc:p49720] Rooted 63.9104 66.0131 1.0329
1696 60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403] 56.6562 54.8538 1.03286
polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361] Ranked 217.624 214.69 1.01367
proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Squared 26211.3 28968.8 1.1052
wiskott-aldrich syndrome protein family member 2 (wasp-family protein member 2) (verprolin homology domain-containing protein 2). [swissprot;acc:q9y6w5] Measured 6304.22 6738.77 1.06893
1697 homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8] Squared 26192.8 28939.3 1.10486
hskin17 protein. [refseq;acc:nm_012311] Ranked 217.624 214.69 1.01367
splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955] Rooted 56.6562 54.8538 1.03286
wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6] Measured 6304.21 6738.77 1.06893
1698 amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203] Rooted 56.6562 54.8538 1.03286
carnitine o-acetyltransferase (ec 2.3.1.7) (carnitine acetylase) (cat). [swissprot;acc:p43155] Ranked 217.624 214.69 1.01367
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177] Squared 28693.8 31699.9 1.10476
wiskott-aldrich syndrome protein family member 1 (wasp-family protein member 1) (verprolin homology domain-containing protein 1). [swissprot;acc:q92558] Measured 6304.22 6738.77 1.06893
1699 2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694] Squared 28693.8 31699.9 1.10476
polyadenylate-binding protein 4 (poly(a)-binding protein 4) (pabp 4) (inducible poly(a)-binding protein) (ipabp) (activated-platelet protein-1) (app-1). [swissprot;acc:q13310] Ranked 217.624 214.69 1.01367
rest corepressor. [refseq;acc:nm_015156] Measured 6304.21 6738.77 1.06893
sorting nexin 17. [swissprot;acc:q15036] Rooted 56.6562 54.8538 1.03286
1700 jm1 protein. [refseq;acc:nm_014008] Squared 27139.1 29980.5 1.1047
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing gamma polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-gamma) (ptdins-3-kinase c2 gamma) (pi3k-c2gamma). [swissprot;acc:o75747] Measured 6326.24 6762.27 1.06892
polyadenylate-binding protein 1 (poly(a)-binding protein 1) (pabp 1). [swissprot;acc:p11940] Ranked 217.624 214.69 1.01367
tensin. [refseq;acc:nm_022648] Rooted 62.1094 64.1498 1.03285
1701 camp-dependent protein kinase type ii-alpha regulatory chain. [swissprot;acc:p13861] 62.9765 65.0427 1.03281
glucose-6-phosphate 1-dehydrogenase (ec 1.1.1.49) (g6pd). [swissprot;acc:p11413] Ranked 216.079 219.024 1.01363
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Squared 24021.7 26536.2 1.10468
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] Measured 6326.24 6762.27 1.06892
1702 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] Squared 17012 18792.5 1.10466
dna-repair protein xrcc3 (x-ray repair cross-complementing protein 3). [swissprot;acc:o43542] Ranked 216.079 219.024 1.01363
dynamin 1-like protein isoform 3; dynamin-like protein. [refseq;acc:nm_005690] Measured 6326.24 6762.27 1.06892
protein kinase pkx1 (ec 2.7.1.-). [swissprot;acc:p51817] Rooted 62.9822 65.0473 1.03279
1703 atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762] Ranked 216.079 219.024 1.01363
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612] Rooted 62.9823 65.0473 1.03279
guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992] Squared 2612.13 2364.75 1.10461

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/