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

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Showing element 951 to 1000 of 77072 in total

Filtered  : 0
Value Type  : Measured

green	Network Comparison Type	network_comparison	Rank	Interaction Map	red	description
875.806	Divided	1.02274	673	Low confidence	856.334	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]
	Subtracted	19.472	745
887.413	Divided	1.18697	210	High confidence	1053.33	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]
	Subtracted	165.917	193
888.843	Divided	1.05296	548	Low confidence	935.913	lactotransferrin precursor (lactoferrin) [contains: lactoferroxin a; lactoferroxin b; lactoferroxin c]. [swissprot;acc:p02788]
	Subtracted	47.07	611
889.914	Divided	1.03208	623		862.25	camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]
	Subtracted	27.664	695
891.114	Divided	1.30385	141	High confidence	1161.88	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]
	Subtracted	270.766	117
898	Divided	1.78508	67		1603	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
	Subtracted	705	35
898.833	Divided	1.06564	349		957.833	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]
	Subtracted	59	345
901.565	Divided	1.12455	359	Low confidence	801.714	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]
	Subtracted	99.851	438
904.149	Divided	1.21678	191	High confidence	743.066	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]
	Subtracted	161.083	197
917.583	Divided	1.0728	467	Low confidence	984.387	metaxin 1. [swissprot;acc:q13505]
	Subtracted	66.804	534
923.065	Divided	1.98228	65		465.658	bet5 homolog (multiple myeloma protein 2) (mum-2). [swissprot;acc:q9y5r8]
	Subtracted	457.407	39
925.298	Divided	1.71412	75	High confidence	1586.07	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]
	Subtracted	660.772	36
931.405	Divided	1.05332	377		884.254	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]
	Subtracted	47.151	371
934.348	Divided	2.79409	37		334.401	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]
	Subtracted	599.947	45
936.963	Divided	1.05276	550	Low confidence	890.008	40s ribosomal protein s28. [swissprot;acc:p25112]
	Subtracted	46.955	612
937.501	Divided	1.32453	130		707.801	phosphatidylinositol 4-kinase alpha (ec 2.7.1.67) (pi4-kinase) (ptdins-4-kinase) (pi4k-alpha). [swissprot;acc:p42356]
	Subtracted	229.7	251
943.423	Divided	1.19157	206	High confidence	1124.15	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]
	Subtracted	180.727	177
944.615	Divided	1.25474	158	Low confidence	752.839	rho guanine nucleotide exchange factor (gef) 12; leukemia-associated rho guanine nucleotide exchange factor. [refseq;acc:nm_015313]
	Subtracted	191.776	287
945.391	Divided	1.26875	149		745.137	glycine cleavage system h protein, mitochondrial precursor. [swissprot;acc:p23434]
	Subtracted	200.254	277
950.464	Divided	1.19021	302		798.57	60s ribosomal protein l36. [swissprot;acc:q9y3u8]
	Subtracted	151.894	326
952.163	Divided	1.10589	396		1052.99	zinc finger protein 232. [swissprot;acc:q9uny5]
	Subtracted	100.827	435
952.394	Divided	1.18614	303		802.936	ba161i19.3 (similar to ribosomal protein l36). [sptrembl;acc:q8wx03]
	Subtracted	149.458	328
954.304	Divided	1.00761	787		947.1	guanine nucleotide-binding protein g(s), alpha subunit (adenylate cyclase-stimulating g alpha protein). [swissprot;acc:p04895]
	Subtracted	7.204	795
958.097	Divided	1.05585	519		1011.61	keratin associated protein 9.2. [refseq;acc:nm_031961]
	Subtracted	53.513	574
958.724	Divided	1.05539	523		1011.83	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]
	Subtracted	53.106	581

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.