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 2630 to 2679 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
165	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Rooted	Divided	1	55.6486	65.1478	1.1707
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Measured			23693.7	18263	1.29736
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]			0	1002.2	793.818	1.26251
	musashi 1. [refseq;acc:nm_002442]	Rooted	Subtracted	1	54.9787	66.2416	11.2629
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Squared	Divided	0	54383.4	34012.2	1.59894
	prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	Measured	Subtracted		293	493	200
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Ranked	Divided		13255.4	15183.2	1.14544
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Rooted	Subtracted		26.1597	29.2445	3.0848
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Ranked		1	133	105	28
	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	Squared			59016.1	75486.9	16470.8
	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	Rooted	Divided	0	17.1346	14.7899	1.15853
166	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	Squared	Subtracted	1	69201.8	53013.4	16188.4
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Measured	Divided	0	5629.62	7099.51	1.2611
	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Ranked	Subtracted		14554.5	16027.9	1473.4
	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]		Divided	1	209.299	249.187	1.19058
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Measured	Subtracted		4489.19	2765.82	1723.37
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Squared	Divided		173408	242989	1.40126
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]			0	220.039	350.57	1.59322
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Rooted		1	55.6495	65.1458	1.17064
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Measured			23693.7	18263	1.29736
	mesoderm induction early response 1. [refseq;acc:nm_020948]	Rooted	Subtracted	0	43.1585	40.0869	3.0716
	my016 protein. [sptrembl;acc:q9h3k6]	Ranked	Divided		5561.19	6366.91	1.14488
	neurocalcin delta. [swissprot;acc:p29554]	Squared	Subtracted		4946.59	5466.65	520.06
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Ranked		1	312	284	28
	nuclear protein ukp68. [refseq;acc:nm_024824]	Rooted			54.9787	66.2416	11.2629
	zinc finger imprinted 2. [swissprot;acc:q9nzv7]		Divided	0	17.1395	14.7969	1.15832
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Measured	Subtracted		320.012	120.429	199.583
167	60s ribosomal protein l15. [swissprot;acc:p39030]	Ranked			11745.2	13203.1	1457.9
	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]			1	133	105	28
	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	Squared			64975.9	81151.2	16175.3
	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	Rooted		0	56.92	59.965	3.045
	daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	Measured			671.769	472.945	198.824
	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Squared	Divided		168.446	105.991	1.58925
	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	Subtracted	1	55.6161	66.7332	11.1171
	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Ranked	Divided		209.299	249.187	1.19058
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Squared			173408	242989	1.40126
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Rooted			55.65	65.1448	1.17062
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Measured			23693.7	18263	1.29736
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]		Subtracted		4489.19	2765.82	1723.37
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Ranked	Divided	0	12157.6	13890.3	1.14252
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	Rooted			52.8301	45.6332	1.15771
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Squared	Subtracted		956.375	441.285	515.09
	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	Measured	Divided		331.61	417.983	1.26047
168	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	Squared	Subtracted	1	69165.6	52992.1	16173.5
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Ranked			312	284	28
	fos-related antigen 2. [swissprot;acc:p15408]		Divided	0	7091.75	6217.28	1.14065
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]			1	82.5916	98.0548	1.18722
	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	Squared	Subtracted	0	1679.15	1177.18	501.97
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Measured		1	4489.19	2765.82	1723.37
	importin 4. [refseq;acc:nm_024658]	Ranked		0	12337.6	13788.9	1451.3

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.