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	Rank	Gene	Interaction Map	network_comparison	description	red	Network Comparison Type

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Showing element 951 to 1000 of 77072 in total

Filtered  : 0
Value Type  : Measured

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

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.