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

Results: HTML CSV LaTeX

Showing element 1160 to 1209 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
145	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	Measured	Divided	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
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Rooted		55.0737	66.0298	1.19894
	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		265.632	319.531	1.20291
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	Rooted	Subtracted	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
	signal transducing adaptor molecule 2; stam-like protein containing sh3 and itam domains 2. [refseq;acc:nm_005843]		Subtracted	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
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Measured		2671	871	1800
147	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	Rooted		41.6851	28.9509	12.7342
	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]		Divided	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
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]		Divided	50.7983	42.3003	1.2009
	protein x 0004. [refseq;acc:nm_016301]	Measured	Subtracted	2671	871	1800
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]		Divided	11068	8508.5	1.30082
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Squared		103496	146848	1.41888
148	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Measured		11068	8508.5	1.30082
	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]	Ranked	Subtracted	226.582	198.444	28.138
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Rooted	Divided	42.0577	50.424	1.19892
	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]		Subtracted	41.6879	28.9554	12.7325
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Squared	Divided	103496	146848	1.41888
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]		Subtracted	70011	49783	20228
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Ranked	Divided	296.677	247.559	1.19841
	symplekin. [swissprot;acc:q92797]	Measured	Subtracted	15213.4	13418.1	1795.3
149	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Squared	Divided	103496	146848	1.41888
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Ranked		142	170	1.19718
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Rooted		42.0684	50.4323	1.19882
	metaxin 1. [swissprot;acc:q13505]	Squared	Subtracted	60401.6	79875.7	19474.1
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Measured	Divided	11068	8508.5	1.30082
	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	Rooted	Subtracted	41.6969	28.9696	12.7273
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Ranked		226.582	198.444	28.138
	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648]	Measured		11736.6	13531.9	1795.3
150	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410]	Rooted		42.2825	54.9687	12.6862
	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	Squared		57913.5	76336.3	18422.8
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Ranked	Divided	55	46	1.19565
	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	Squared		121200	85473.4	1.41799
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Ranked	Subtracted	226.582	198.444	28.138
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured	Divided	11068	8508.5	1.30082
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Rooted		63.5827	53.0856	1.19774
	small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641]	Measured	Subtracted	4172.91	5954.48	1781.57
151	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Rooted	Divided	38.8223	46.4975	1.1977
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared		250303	354894	1.41786
	epoxide hydrolase 1 (ec 3.3.2.3) (microsomal epoxide hydrolase) (epoxide hydratase). [swissprot;acc:p07099]		Subtracted	87971.9	69563.1	18408.8
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Rooted		50.3065	62.9788	12.6723
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Ranked	Divided	55	46	1.19565
	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	Measured	Subtracted	14830.5	13050.3	1780.2
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Ranked		226.582	198.444	28.138
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Measured	Divided	4578.09	5939.91	1.29746
152	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]		Subtracted	5136.78	6895.98	1759.2

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.