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 1714 to 1763 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
108	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Measured	Divided	0	292	421	1.44178
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Squared	Subtracted		1797.76	558.241	1239.52
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Rooted	Divided		13.7191	17.6786	1.28861
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Measured		1	4366.44	5899.76	1.35116
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	Ranked			252.296	201.995	1.24902
	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]		Subtracted		209.299	249.187	39.888
	microtubule-associated protein, rp/eb family, member 2; t-cell activation protein, eb1 family; apc-binding protein eb1. [refseq;acc:nm_014268]	Measured		0	482.426	192.295	290.131
	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	Squared	Divided	1	19321	12542.6	1.54043
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Ranked		0	10585.3	12769.1	1.2063
	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	Measured	Subtracted	1	14021.4	11523	2498.4
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Squared			78383	108483	30100
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Rooted			63.7475	48.1615	15.586
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]			0	4.83477	9.39626	4.56149
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Squared	Divided		795.24	1645.86	2.06964
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	Rooted		1	49.2925	62.397	1.26585
109	44050 protein. [refseq;acc:nm_178832]	Measured	Subtracted		17385.9	14889.2	2496.7
	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Squared		0	5219.15	3979.89	1239.26
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]			1	88432.6	58423.3	30009.3
	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Measured	Divided	0	100	144	1.44
	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Ranked			14466.8	12031.7	1.20239
	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]		Subtracted	1	209.299	249.187	39.888
	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]		Divided		266.933	333.281	1.24856
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	Squared			19321	12542.6	1.54043
	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]	Rooted	Subtracted		30.8986	46.4619	15.5633
	protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031]	Ranked		0	9940.69	11929	1988.31
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Rooted	Divided		2.64575	3.38392	1.279
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Measured		1	4366.44	5899.76	1.35116
	soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825]	Rooted	Subtracted	0	21.0524	16.4963	4.5561
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Measured			934.726	1222.89	288.164
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	Rooted	Divided	1	49.2923	62.3969	1.26585
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Squared		0	16.4056	33.4891	2.04132
110	deltex 2. [refseq;acc:nm_020892]	Ranked		1	333.144	267.393	1.2459
	dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	Measured	Subtracted	0	528.5	816.5	288
	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	Ranked	Divided		12584.5	10470.6	1.20189
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Rooted	Subtracted		54.8943	59.4407	4.5464
	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	Ranked		1	209.299	249.187	39.888
	importin 7; ran-binding protein 7. [refseq;acc:nm_006391]			0	14864.7	16820.7	1956
	junctophilin 3 (junctophilin type 3) (jp-3). [swissprot;acc:q8wxh2]	Rooted		1	33.9632	18.4255	15.5377
	myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535]	Squared	Divided		19321	12542.6	1.54043
	nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]	Measured	Subtracted		17385.9	14889.2	2496.7
	pnas-18. [sptrembl;acc:q9bzu3]	Squared			87787.3	58155.8	29631.5
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Measured	Divided		4366.44	5899.76	1.35116
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Rooted		0	7.7419	6.06104	1.27732
	spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813]	Measured			1833	2637	1.43863
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Squared	Subtracted		5219.15	3979.89	1239.26
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	Rooted	Divided	1	49.293	62.3973	1.26585
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	Squared		0	16.4056	33.4891	2.04132
111	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]		Subtracted	1	79779.8	108084	28304.2
	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Rooted		0	35.0775	30.5361	4.5414
	deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	Ranked	Divided	1	332.925	267.274	1.24563

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.