MK5 Microarray Data

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

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Showing element 1358 to 1407 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
1358	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	214.987	210.359	1.022
1359	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	228.642	223.726	1.02197
1360	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897]	223.89	228.805	1.02195
1361	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]	214.971	210.354
1362	peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911]	228.644	223.736	1.02194
1363	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	218.591	213.899
1364	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896]	223.885	228.797
1365	atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]	228.644	223.736
1366	activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	223.884	228.795
1367	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610]	223.887	228.799
1368	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]	228.644	223.736
1369	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]
1370	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	205.185	200.784	1.02192
1371	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711]	228.646	223.744	1.02191
1372	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524]	216.542	211.908	1.02187
1373	glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
1374	asc-1 complex subunit p100. [refseq;acc:nm_032204]
1375	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071]
1376	eyes absent homolog 3. [swissprot;acc:q99504]	218.537	213.91	1.02163
1377	sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467]	218.471	213.876	1.02148
1378	sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9]	218.47
1379	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]		213.875
1380	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818]		213.876
1381	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156]
1382	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]
1383	adaptor-associated kinase 1. [refseq;acc:nm_014911]
1384	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]	218.471
1385	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	218.47	213.875
1386	rho-gtpase activating protein 10. [refseq;acc:nm_020824]		213.876
1387	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2]		213.875
1388	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	218.471	213.876
1389	2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [swissprot;acc:p21953]	218.47	213.875
1390	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316]
1391	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492]
1392	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]	218.471	213.876
1393	membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835]	218.47	213.875
1394	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]
1395	growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861]		213.876
1396	eyes absent homolog 1. [swissprot;acc:q99502]	218.463	213.872	1.02147
1397	40s ribosomal protein s8. [swissprot;acc:p09058]	218.64	214.049	1.02145
1398	eyes absent homolog 4. [swissprot;acc:o95677]	218.449	213.864	1.02144
1399	eyes absent homolog 2. [swissprot;acc:o00167]	218.417	213.848	1.02137
1400	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544]	218.667	214.118	1.02125
1401	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336]	218.657	214.11	1.02124
1402	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	209.682	205.329	1.0212
1403	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	184.656	180.823
1404	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427]	232.752	237.65	1.02104
1405	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	245.532	240.483	1.021
1406	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	212.833	208.456
1407	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]	206.104	210.424	1.02096

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.