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 2775 to 2824 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
174	kappa b-ras 1. [refseq;acc:nm_020345]	Ranked	Subtracted	0	12657.7	11299.1	1358.6
	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	Squared			58677.8	58207.8	470
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Ranked		1	228.1	200.968	27.132
	mad protein (max dimerizer). [swissprot;acc:q05195]	Measured	Divided		4455.95	5774.03	1.2958
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	Rooted			145.551	168.796	1.1597
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Ranked		0	13248.5	11666.4	1.13561
	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]	Rooted	Subtracted	1	37.3005	48.4141	11.1136
	sedlin. [swissprot;acc:o14582]	Squared	Divided		112820	157033	1.39189
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	Measured	Subtracted		4556.83	2945.38	1611.45
	uridine kinase-like 1. [swissprot;acc:q9nwz5]			0	633.433	821.711	188.278
175	cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653]	Ranked	Divided	1	199.949	234.187	1.17123
	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	Measured		0	1382.5	1107	1.24887
	cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	Squared			48.5538	75.7214	1.55954
	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	Rooted	Subtracted	1	37.3005	48.4141	11.1136
	fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]	Squared			71576.8	56326.7	15250.1
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Measured		0	2056.14	2244.06	187.92
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Squared			3693.52	3232.47	461.05
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Ranked		1	228.085	201.006	27.079
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Measured	Divided		4456.67	5773.77	1.29553
	nucleoporin nup43 (p42). [swissprot;acc:q8nfh3]	Rooted		0	61.6393	70.9983	1.15183
	orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [swissprot;acc:q9y466]		Subtracted		47.6356	44.6445	2.9911
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]		Divided	1	145.551	168.796	1.1597
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	Ranked	Subtracted	0	11573.8	10231.3	1342.5
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Measured		1	4556.99	2945.8	1611.19
	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	Squared	Divided		112820	157033	1.39189
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Ranked		0	13248.5	11666.4	1.13561
176	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]		Subtracted		11935.1	10592.8	1342.3
	40s ribosomal protein s29. [swissprot;acc:p30054]	Measured			1711.6	1895.38	183.78
	bet3 homolog. [swissprot;acc:o43617]	Squared	Divided	1	112820	157033	1.39189
	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	Rooted	Subtracted		37.3005	48.4141	11.1136
	cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	Squared	Divided	0	48.5538	75.7214	1.55954
	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	Ranked			13068	11528	1.13359
	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	Rooted			20.3469	17.7078	1.14904
	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Ranked		1	275.754	235.908	1.1689
	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]		Subtracted		271.016	244.167	26.849
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Measured			10235.2	11830.8	1595.6
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Squared		0	3680.47	3222.63	457.84
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Rooted			23.871	20.9159	2.9551
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Measured	Divided	1	4456.93	5773.67	1.29544
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted			145.551	168.796	1.1597
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Squared	Subtracted		71576.8	56326.7	15250.1
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Measured	Divided	0	3023.85	2436.4	1.24111
177	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]				4131.06	3340.03	1.23683
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Squared	Subtracted	1	9924.76	25146.6	15221.8
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Ranked	Divided		229.406	196.695	1.1663
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Rooted		0	20.3458	17.7104	1.14881
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Squared			73.1683	109.766	1.50019
	keratin associated protein 1.5. [refseq;acc:nm_031957]		Subtracted		3680.43	3222.6	457.83
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Measured		1	4110.14	5694.99	1584.85
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]		Divided		4457.06	5773.63	1.29539

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.