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 5262 to 5311 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2631	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]	Subtracted	4180.32	4253.46	73.14
2632	histone h4. [swissprot;acc:p02304]	Divided	6072.17	6155.08	1.01365
	meiotic recombination protein spo11. [swissprot;acc:q9y5k1]	Subtracted	4180.32	4253.46	73.14
2633	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	Divided	4000.73	3947.54	1.01347
	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	Subtracted	6742.48	6814.18	71.7
2634	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]		4367.69	4438.77	71.08
	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	Divided	3640.58	3688.96	1.01329
2635	hiv-1 tat interactive protein 2, 30kda; tat-interacting protein (30kd); hiv-1 tat interactive protein 2, 30 kda; hiv-1 tat interactive protein 2, 30 kd. [refseq;acc:nm_006410]		7197.82	7291.66	1.01304
	nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221]	Subtracted	8290.91	8220.11	70.8
2636	ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	Divided	7017.82	7108.89	1.01298
	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Subtracted	3899.28	3829.53	69.75
2637	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]		3926.4	3857.88	68.52
	protein kinase nyd-sp25. [refseq;acc:nm_033516]	Divided	6527.56	6608.61	1.01242
2638	b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	Subtracted	8278.73	8211.05	67.68
	insulin gene enhancer protein isl-2 (islet-2). [swissprot;acc:q96a47]	Divided	7433.72	7525.14	1.0123
2639	nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838]	Subtracted	8277.7	8210.29	67.41
	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	Divided	6742.48	6814.18	1.01063
2640	nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653]	Subtracted	8277.66	8210.26	67.4
	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]	Divided	5339.06	5395.25	1.01052
2641	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]		3377.01	3411.47	1.0102
	nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653]	Subtracted	8277.6	8210.21	67.39
2642	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584]		4582.38	4649.17	66.79
	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	Divided	5935.71	5876.22	1.01012
2643	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]
	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	Subtracted	4450.84	4517.54	66.7
2644	jm4 protein. [refseq;acc:nm_007213]		7133.06	7067.09	65.97
	ubiquilin 1 isoform 1. [refseq;acc:nm_013438]	Divided	9125.08	9217	1.01007
2645	ataxin-1 ubiquitin-like interacting protein. [refseq;acc:nm_020131]		9128.19	9218.44	1.00989
	cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407]	Subtracted	7118.22	7055.43	62.79
2646	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]		8936.97	8999.55	62.58
	mct-1 protein. [refseq;acc:nm_014060]	Divided	4778.28	4732.13	1.00975
2647	highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	Subtracted	4508.81	4446.41	62.4
	mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]	Divided	4778.28	4732.13	1.00975
2648	tumor protein d54 (hd54) (d52-like 2). [swissprot;acc:o43399]		6365.03	6424.56	1.00935
		Subtracted			59.53
2649	jm4 protein. [refseq;acc:nm_007213]	Divided	7133.06	7067.09	1.00933
	vam6/vps39-like protein (hvam6p). [swissprot;acc:q96jc1]	Subtracted	5935.71	5876.22	59.49
2650	beclin 1 (coiled-coil myosin-like bcl2-interacting protein) (protein gt197). [swissprot;acc:q14457]	Divided	9150.44	9234.09	1.00914
	microtubule-associated protein 4 (map 4). [swissprot;acc:p27816]	Subtracted	5935.71	5876.22	59.49
2651	26s protease regulatory subunit 8 (proteasome subunit p45) (thyroid hormone receptor interacting protein 1) (trip1) (msug1 protein) (tat-binding protein homolog 10) (tbp10) (p45/sug). [swissprot;acc:p47210]	Divided	9150.44	9234.09	1.00914
	tumor protein d52 (n8 protein). [swissprot;acc:p55327]	Subtracted	6349.55	6407.25	57.7
2652		Divided			1.00909
	tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890]	Subtracted	6349.23	6406.72	57.49
2653	polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]		3985.17	3928.38	56.79
	tumor protein d53 (hd53) (d52-like 1). [swissprot;acc:q16890]	Divided	6349.23	6406.72	1.00905
2654	40s ribosomal protein s9. [swissprot;acc:p46781]	Subtracted	3933.74	3877.14	56.6
	cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407]	Divided	7118.22	7055.43	1.0089
2655	nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221]		8290.91	8220.11	1.00861
	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]	Subtracted	5339.06	5395.25	56.19
2656	iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399]		8222.61	8169.38	53.23

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.