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 243 to 292 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
122	fos-related antigen 2. [swissprot;acc:p15408]	Subtracted	4941.95	7037.11	2095.16
	high-mobility group 20a. [refseq;acc:nm_018200]	Divided	5140.14	6893.53	1.34112
123	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		24260.3	18172.1	1.33503
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	Subtracted	4942.49	7037.32	2094.83
124	fos-related antigen 1 (fra-1). [swissprot;acc:p15407]		4944.3	7038.04	2093.74
	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	Divided	24255.7	18168.9	1.33501
125	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	Subtracted	12471.7	14561.7	2090
	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	Divided	24255.7	18168.9	1.33501
126	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]		24250	18164.9	1.33499
	rad50-interacting protein 1. [refseq;acc:nm_021930]	Subtracted	450.5	2394.5	1944
127	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]
	transcription factor jun-d. [swissprot;acc:p17535]	Divided	5638.2	7523.39	1.33436
128	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]		4355.61	5810.82	1.3341
	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987]	Subtracted	11004.2	12944.2	1940
129	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Divided	4358.13	5811.49	1.33348
	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	Subtracted	15274.9	13346.9	1928
130	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Divided	2234.68	2978.53	1.33287
	p66 alpha. [refseq;acc:nm_017660]	Subtracted	12839	10911.1	1927.9
131	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Divided	2234.73	2978.57	1.33285
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Subtracted	12839	10911.1	1927.9
132	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Divided	2236.61	2980.35	1.33253
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Subtracted	12839	10911.1	1927.9
133	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]		12798.9	10887.2	1911.7
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Divided	23421.5	17580.4	1.33225
134	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	Subtracted	12796.8	10886	1910.8
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Divided	21785.2	16426.1	1.32626
135	apg3p; pc3-96 protein. [refseq;acc:nm_022488]
	transcription factor jun-b. [swissprot;acc:p17275]	Subtracted	5579.18	7488.4	1909.22
136	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]		12787.6	10880.5	1907.1
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	Divided	3620.77	4763.34	1.31556
137	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]
	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	Subtracted	12786.6	10879.9	1906.7
138	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592]	Divided	2755.15	2094.3	1.31555
	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	Subtracted	15182.5	13277.9	1904.6
139	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]		12780.7	10876.4	1904.3
	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	Divided	2759.61	2099.49	1.31442
140	homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	Subtracted	2597.5	698.5	1899
	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]	Divided	2760.28	2100.27	1.31425
141	hbs1-like. [refseq;acc:nm_006620]	Subtracted	2597.5	698.5	1899
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Divided	4405.4	5782.08	1.3125
142	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]		9276.47	7090.37	1.30832
	transcription factor jun-d. [swissprot;acc:p17535]	Subtracted	5638.2	7523.39	1885.19
143	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Divided	9275.1	7089.65	1.30826
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Subtracted	15427.2	13572.8	1854.4
144	nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483]		4133.47	5945.32	1811.85
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Divided	3349.9	4362.61	1.30231
145	nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085]	Subtracted	4136.36	5943.56	1807.2
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	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
	xpa binding protein 1; mbd2 interactor protein; putative atp(gtp)-binding protein. [refseq;acc:nm_007266]	Subtracted	2671	871	1800

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.