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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Filtered	Gene	Value Type	Network Comparison Type	Interaction Map	network_comparison	Rank	description	green	red

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Showing element 3682 to 3731 of 77072 in total

Filtered  : 0
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : Low confidence

network_comparison	Rank	description	green	red
1.09624	354	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	13350.4	14635.3
1.09639	353	neurocalcin delta. [swissprot;acc:p29554]	12162.7	13335.1
1.09654	352	rho gdp-dissociation inhibitor 1 (rho gdi 1) (rho-gdi alpha). [swissprot;acc:p52565]	8744.24	9588.38
1.09678	350	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	17178.7	15662.8
	351	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]
1.0969	349		17176.5	15659.1
1.09738	348	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	14425.4	13145.3
1.09742	347	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	12389.7	13596.7
1.09754	346	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	10994.9	12067.3
1.09845	345	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	10927.4	12003.2
1.09891	344	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	12743.3	14003.7
1.09942	343	phosphoinositide-3-kinase, regulatory subunit 4, p150; phosphatidylinositol 3-kinase-associated p150. [refseq;acc:nm_014602]	10888	9903.38
1.10062	342	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	13531.6	12294.5
1.10158	341	e1a binding protein p400; p400 swi2/snf2-related protein; cagh32 protein; trinucleotide repeat containing 12. [refseq;acc:nm_015409]	10576.1	9600.88
1.10193	340	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]	10024.6	9097.31
1.10269	339	hexokinase, type i (ec 2.7.1.1) (hk i) (brain form hexokinase). [swissprot;acc:p19367]	13838.9	12550.1
1.10322	338	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	11207.9	12364.8
1.10323	337	tigger transposable element derived 7; jerky (mouse) homolog-like. [refseq;acc:nm_033208]	11207.7	12364.7
1.10331	336	napsin 1 precursor (ec 3.4.23.-) (napsin a) (napa) (ta01/ta02) (aspartyl protease 4) (asp 4) (asp4). [swissprot;acc:o96009]	11424.6	10354.8
1.10355	334	tigger transposable element derived 6. [refseq;acc:nm_030953]	11200.2	12360
	335	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	11370.4	10303.5
1.10588	333	guanine nucleotide-binding protein g(s), alpha subunit (adenylate cyclase-stimulating g alpha protein). [swissprot;acc:p04895]	13965.7	12628.6
1.10674	332	stromal membrane-associated protein; stromal membrane-associated protein smap1a. [refseq;acc:nm_021940]	13938.9	12594.6
1.10682	331	wd-repeat protein 5 (wd-repeat protein big-3). [swissprot;acc:q9ugp9]	16345.9	14768.3
1.10708	330	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]	12125.1	10952.3
1.10709	329	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]	11839.1	10693.9
1.10742	328	double-stranded rna-specific editase 1 (ec 3.5.-.-) (dsrna adenosine deaminase) (rna editing deaminase 1) (rna editing enzyme 1). [swissprot;acc:p78563]	8611	9536
1.10795	327	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	17469.2	19355
1.10849	326	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	11061.5	9978.85
1.10865	325	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	12202.2	11006.4
1.10882	324	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	9927.8	8953.45
1.10892	323	dna helicase homolog (fragment). [sptrembl;acc:q9y645]	18475.5	16660.8
1.10947	322	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	11238.6	10129.7
1.10952	321	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	10410.1	11550.2
1.11002	320	ubiquitin-conjugating enzyme hbuce1. [refseq;acc:nm_015983]	10848.6	12042.2
1.11025	319	fos-related antigen 2. [swissprot;acc:p15408]	6959.54	7726.82
1.11058	318	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	9342.88	10376
1.11095	317	putative dynein light chain protein dj8b22.1. [swissprot;acc:q9y3p0]	12079.7	13420
1.11154	316	myosin vi. [swissprot;acc:q9um54]	11250.5	10121.5
1.11156	315	g protein-coupled receptor 142. [refseq;acc:nm_181790]	11067.8	9957.01
1.11195	314	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	10922.5	12145.3
1.11196	313	metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832]	16405	18241.7
1.11245	312	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	13653	15188.3
1.11265	311	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	13355.2	12003.1
1.11276	310	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	11164.2	10032.9
1.11345	309	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	11679.4	10489.4
1.11361	307	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	6716	7479
	308	dc11 protein. [refseq;acc:nm_020186]
1.1144	304	maspin precursor (protease inhibitor 5). [swissprot;acc:p36952]	15123	16853
	305	serpin b11. [swissprot;acc:q96p15]

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.