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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 2825 to 2874 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
177	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted	Divided	1	145.551	168.796	1.1597
	mstp028 protein. [refseq;acc:nm_031954]		Subtracted	0	64.9832	62.0398	2.9434
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Measured			1124.15	943.423	180.727
	pnas-18. [sptrembl;acc:q9bzu3]	Ranked			12602.7	13939.6	1336.9
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]		Divided		14922.7	13174.5	1.1327
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Rooted	Subtracted	1	37.3005	48.4141	11.1136
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Squared	Divided		78383	108483	1.38401
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	Ranked	Subtracted		241.07	267.88	26.81
178	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Squared			9924.76	25146.6	15221.8
	carboxypeptidase b precursor. [refseq;acc:nm_020361]		Divided		25326.4	18354.1	1.37988
	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Rooted		0	35.0775	30.5361	1.14872
	cullin homolog 1 (cul-1). [swissprot;acc:q13616]		Subtracted	1	37.3005	48.4141	11.1136
	dc11 protein. [refseq;acc:nm_020186]	Squared	Divided	0	73.1683	109.766	1.50019
	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]	Ranked	Subtracted	1	241.07	267.88	26.81
	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Measured	Divided	0	498.07	615.233	1.23523
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Ranked		1	226.887	194.72	1.1652
	integral membrane protein cii-3b. [sptrembl;acc:o75609]			0	14951.6	13204.2	1.13234
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Squared	Subtracted		3680.43	3222.6	457.83
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Rooted			12.6886	9.74679	2.94181
	mstp028 protein. [refseq;acc:nm_031954]	Measured			9988.45	9808.48	179.97
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]		Divided	1	21591.5	27904.5	1.29238
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]		Subtracted		10908.6	12491.8	1583.2
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Rooted	Divided		45.7414	52.932	1.1572
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Ranked	Subtracted	0	10899.5	12217.4	1317.9
179	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Measured		1	4266.04	5843.51	1577.47
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Ranked		0	12190.3	13497.2	1306.9
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Measured	Divided		556	681	1.22482
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Rooted	Subtracted	1	55.0737	66.0298	10.9561
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Ranked	Divided		226.884	194.79	1.16476
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Rooted	Subtracted	0	23.8722	20.933	2.9392
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Squared			3680.39	3222.57	457.82
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]		Divided	1	25326.3	18354.1	1.37987
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Ranked		0	9473.01	10723.7	1.13203
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Measured		1	21591.5	27904.5	1.29238
	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	Rooted			50.272	43.4634	1.15665
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Ranked	Subtracted		227.357	254.15	26.793
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Measured		0	304.664	483.809	179.145
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Squared		1	9924.76	25146.6	15221.8
	suppressor of actin 1. [refseq;acc:nm_014016]		Divided	0	0.284967	0.426714	1.49742
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Rooted			32.6268	28.4118	1.14835
180	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Squared	Subtracted	1	9924.76	25146.6	15221.8
	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	Measured			10872.4	12447	1574.6
	dc11 protein. [refseq;acc:nm_020186]		Divided	0	556	681	1.22482
	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Rooted		1	50.2801	43.4779	1.15645
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Squared	Subtracted	0	3680.39	3222.57	457.82
	keratin associated protein 1.5. [refseq;acc:nm_031957]	Rooted			23.8722	20.9331	2.9391
	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]			1	88.4361	77.5112	10.9249
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Measured	Divided		21591.5	27904.5	1.29238
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Squared			25326.2	18354.1	1.37987
	pp3111 protein. [refseq;acc:nm_022156]	Ranked	Subtracted		227.357	254.15	26.793

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.