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 800 to 849 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
50	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Measured	Subtracted	0	4962.34	5469.68	507.34
51	adapter-related protein complex 1 sigma 1b subunit (sigma-adaptin 1b) (adaptor protein complex ap-1 sigma-1b subunit) (golgi adaptor ha1/ap1 adaptin sigma-1b subunit) (clathrin assembly protein complex 1 sigma- 1b small chain) (sigma 1b subunit of ap-1 clathrin) (dc22). [swissprot;acc:p56377]	Squared	Divided		0.872309	3.99932	4.58475
	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]			1	28994.2	17134.8	1.69212
	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]	Ranked	Subtracted		350	290	60
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Squared		0	21584.2	16770.2	4814
	fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917]	Measured		1	23640.2	19479.8	4160.4
	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Ranked		0	12143.8	8356.02	3787.78
		Rooted			14.8299	22.5463	7.7164
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]			1	137.446	120.823	16.623
	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Squared			173408	242989	69581
	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Ranked	Divided	0	7168	5102	1.40494
	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]	Rooted		1	27.7254	44.0299	1.58807
	nanos (fragment). [sptrembl;acc:q8wy41]			0	19.4165	12.2882	1.58009
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Measured		1	779.167	1390.33	1.78438
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]			0	184.422	88.5622	2.0824
	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]		Subtracted		4962.34	5469.68	507.34
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Ranked	Divided	1	133	105	1.26667
52	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]			0	3284	4554.5	1.38688
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Measured		1	779.167	1390.33	1.78438
	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]		Subtracted		23422.4	19380.3	4042.1
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		Divided	0	999.28	481.725	2.07438
	fos-related antigen 2. [swissprot;acc:p15408]	Squared	Subtracted		6691.06	2188.28	4502.78
	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]	Rooted			0	7.68115	7.68115
	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	Ranked			11461	15180	3719
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Squared		1	173408	242989	69581
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Rooted			137.446	120.823	16.623
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]		Divided	0	16.3095	25.3969	1.55718
	neuralized-like. [refseq;acc:nm_004210]			1	27.9107	44.1656	1.58239
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Squared			28994.2	17134.8	1.69212
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	Ranked	Subtracted		350	290	60
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Squared	Divided	0	1.22698	5.39669	4.39835
	udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	Measured	Subtracted		2230.13	1729.7	500.43
53	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Rooted	Divided		11.844	18.0183	1.5213
	cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	Ranked	Subtracted		7230	10771	3541
	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	Measured	Divided	1	779.167	1390.33	1.78438
	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Rooted	Subtracted	0	25.8353	33.3747	7.5394
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Squared		1	173408	242989	69581
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Measured	Divided	0	420.365	861.814	2.05016
	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181]	Ranked	Subtracted	1	318.982	259.004	59.978
		Rooted	Divided		30.8986	46.4619	1.50369
	necdin. [swissprot;acc:q99608]		Subtracted		137.446	120.823	16.623
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Measured			23326.5	19296.4	4030.1
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Squared	Divided		28994.2	17134.8	1.69212
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]			0	0.458225	0.104379	4.39001
	transcription factor jun-b. [swissprot;acc:p17275]	Ranked		1	201.144	158.868	1.26611
	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]			0	3284	4554.5	1.38688
	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]	Squared	Subtracted		25325.5	29804.9	4479.4
	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	Measured			2230.13	1729.7	500.43
54	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Ranked		1	185.678	245.247	59.569

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.