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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 2294 to 2343 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
144	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Rooted	Subtracted	1	105.205	92.2415	12.9635
	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]	Measured			4133.47	5945.32	1811.85
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Squared	Divided	0	207.597	118.463	1.75242
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]		Subtracted		4275.32	3463.45	811.87
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Measured	Divided	1	3349.9	4362.61	1.30231
	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	Rooted	Subtracted	0	8.48528	12.2882	3.80292
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Squared	Divided	1	123324	86277.9	1.42938
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Rooted			55.6161	66.7332	1.19989
	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]			0	9.72761	8.25872	1.17786
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	Measured			633.433	821.711	1.29723
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Ranked	Subtracted		12225.7	13893.1	1667.4
145	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	Squared	Divided		255.854	146.067	1.75162
	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9]		Subtracted	1	86600.9	65229.9	21371
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Rooted	Divided		55.6161	66.7332	1.19989
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Squared	Subtracted	0	975.125	178.265	796.86
	lamin b2. [swissprot;acc:q03252]	Ranked			12135.4	13802	1666.6
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Rooted			82.3645	86.1594	3.7949
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Ranked		1	239.336	267.881	28.545
	likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033]	Measured	Divided	0	287.903	372.961	1.29544
	methyltransferase like 2. [refseq;acc:nm_018396]	Rooted			5.56776	6.55744	1.17775
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Squared		1	310840	442993	1.42515
	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Measured	Subtracted		4136.36	5943.56	1807.2
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Ranked	Divided		265.639	319.546	1.20293
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Rooted	Subtracted		105.205	92.2415	12.9635
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	Measured		0	2162.33	1932	230.33
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Ranked	Divided		7955.61	6817.49	1.16694
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured		1	16771.5	12889.1	1.30122
146	associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]				11068	8508.5	1.30082
	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	Ranked		0	12577.8	14662.1	1.16571
	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	Measured	Subtracted		17356	17126	230
	cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]		Divided		291.639	377.574	1.29466
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Rooted			13.9593	11.8643	1.17658
	huntingtin interacting protein c. [refseq;acc:nm_012272]			1	55.0737	66.0298	1.19894
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Squared	Subtracted	0	960.518	176.164	784.354
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Ranked	Divided	1	265.632	319.531	1.20291
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Subtracted	0	3208.8	4871.6	1662.8
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Rooted		1	41.6734	28.9323	12.7411
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Squared	Divided		103496	146848	1.41888
	ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108]	Rooted	Subtracted	0	11.6322	7.84538	3.78682
	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]	Squared		1	86281	65058.3	21222.7
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Ranked			239.336	267.879	28.543
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Squared	Divided	0	8.15919	4.74982	1.71779
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Measured	Subtracted	1	2671	871	1800
147	60s ribosomal protein l7. [swissprot;acc:p18124]	Ranked	Divided	0	11080.3	9505.89	1.16562
	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Rooted			21.8452	18.5801	1.17573
	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]		Subtracted	1	41.6851	28.9509	12.7342
	cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	Measured	Divided	0	292.152	378.206	1.29455
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Rooted		1	42.0574	50.4237	1.19893
	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Squared	Subtracted		55630.4	76083.7	20453.3
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Ranked			239.32	267.842	28.522

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.