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

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Showing element 2180 to 2229 of 66312 in total

Filtered  : 1

Rank	description	Network Comparison Type	Value Type	Interaction Map	green	network_comparison	red
137	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Subtracted	Measured	High confidence	10879.9	1906.7	12786.6
	musashi 2 isoform a. [refseq;acc:nm_138962]	Divided	Rooted		66.2416	1.20486	54.9787
	putative adenosylhomocysteinase 2 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:o43865]			Low confidence	64.8315	1.07086	69.4253
	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]		Ranked	High confidence	290	1.2069	350
	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]	Subtracted	Squared	Low confidence	60858	6943.5	67801.5
	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]		Rooted		93.1433	5.0754	88.0679
	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]		Squared	High confidence	92953.5	23404.5	69549
	t-box transcription factor tbx19 (t-box protein 19). [swissprot;acc:o60806]	Divided	Measured	Low confidence	6699.58	1.09121	6139.6
	testican-3 precursor. [swissprot;acc:q9bq16]		Ranked		234.389	1.0635	220.395
	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]	Subtracted	Measured		8050.82	753.25	7297.57
	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]		Ranked		190.88	12.798	203.678
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]		Rooted	High confidence	62.397	13.1045	49.2925
	zinc finger protein 216. [swissprot;acc:o76080]	Divided	Squared	Low confidence	69833.1	1.13346	79152.9
138	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	Subtracted			45948.1	6739.2	52687.3
	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]		Ranked	High confidence	205.556	30.889	174.667
	defender against cell death 1 (dad-1). [swissprot;acc:p46966]		Rooted	Low confidence	74.2065	5.0721	69.1344
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Divided	Measured		7313.38	1.09008	6709
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Subtracted	Squared	High confidence	93908.8	23169.8	70739
	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Divided	Measured		2094.3	1.31555	2755.15
	musashi 1. [refseq;acc:nm_002442]		Rooted		66.2416	1.20486	54.9787
	protein associated with prk1. [refseq;acc:nm_019006]		Squared	Low confidence	69833.1	1.13346	79152.9
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]			High confidence	322755	1.45156	468498
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	Subtracted	Ranked	Low confidence	206.507	12.766	219.273
	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	Divided	Rooted		70.6132	1.07053	65.9611
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]		Ranked	High confidence	234.204	1.20493	194.372
	step ii splicing factor slu7. [refseq;acc:nm_006425]	Subtracted	Measured	Low confidence	10591.9	721.07	9870.83
	transgelin 2 (sm22-alpha homolog). [swissprot;acc:p37802]	Divided	Ranked		205.4	1.0631	218.36
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Subtracted	Measured	High confidence	13277.9	1904.6	15182.5
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]		Rooted		62.3973	13.1043	49.293
139	60s ribosomal protein l37a. [swissprot;acc:p12751]	Divided	Measured	Low confidence	6277.91	1.08946	5762.4
	adiponectin receptor 2. [refseq;acc:nm_024551]	Subtracted	Rooted		71.1967	5.0368	66.1599
	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Divided	Ranked	High confidence	225.68	1.20415	271.752
	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	Subtracted	Measured		10876.4	1904.3	12780.7
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		Ranked		256.835	30.575	287.41
	dnaj homolog subfamily c member 8 (splicing protein spf31) (hspc315). [swissprot;acc:o75937]			Low confidence	207.417	12.421	219.838
	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Divided	Squared	High confidence	56211.1	1.45153	81592.1
	helix-loop-helix protein 2 (hen2) (nescient helix loop helix 2) (nscl- 2). [swissprot;acc:q02577]	Subtracted		Low confidence	49199.8	6664.9	55864.7
	nuclear protein ukp68. [refseq;acc:nm_024824]	Divided	Rooted	High confidence	66.2416	1.20486	54.9787
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]		Measured		2099.49	1.31442	2759.61
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]		Squared	Low confidence	53140.7	1.13344	60231.9
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]		Rooted		70.626	1.07028	65.9882
	signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473]	Subtracted	Squared	High confidence	65369.7	21491.8	86861.5
	testican-1 precursor (spock protein). [swissprot;acc:q08629]	Divided	Ranked	Low confidence	234.111	1.06291	220.254
	vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253]	Subtracted	Measured		8055.84	718.27	7337.57
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]		Rooted	High confidence	62.4167	13.09	49.3267
140	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]		Ranked		198.011	30.295	228.306
	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]		Measured	Low confidence	10529.5	711.5	9818
	c3hc4-type zinc finger protein; likely ortholog of mouse dioxin inducible factor 3. [refseq;acc:nm_024835]		Ranked		207.417	12.421	219.838
	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	Divided	Squared	High confidence	56190.6	1.45091	81527.6
	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]		Rooted		66.7332	1.19989	55.6161

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.