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 3480 to 3529 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
218	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	Ranked	Divided	1	112	126	1.125
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Measured	Subtracted		6417.18	7859.6	1442.42
	suppressor of actin 1. [refseq;acc:nm_014016]	Rooted		0	3.30572	5.87091	2.56519
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]			1	107.178	117.276	10.098
	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	Squared	Divided	0	19.1247	13.8207	1.38377
	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	Measured		1	16070.4	12886	1.24712
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]			0	3645.5	3118.3	1.16907
	udp-n-acetylglucosamine--peptide n-acetylglucosaminyltransferase 110 kda subunit (ec 2.4.1.-) (o-glcnac transferase p110 subunit). [swissprot;acc:o15294]	Squared		1	86600.9	65229.9	1.32763
	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]		Subtracted		46785.7	58383.2	11597.5
219	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Ranked			242.339	266.986	24.647
	cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073]	Squared	Divided		86600.9	65229.9	1.32763
	heat shock factor binding protein 1. [swissprot;acc:o75506]	Rooted	Subtracted	0	20.2359	17.6821	2.5538
	histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]			1	44.963	55.0576	10.0946
	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]		Divided		52.7146	60.0088	1.13837
	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	Squared	Subtracted		46785.7	58383.2	11597.5
	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]			0	68035.1	68294.1	259
	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	Ranked	Divided	1	112	126	1.125
	myosin vi. [swissprot;acc:q9um54]		Subtracted	0	10121.5	11250.5	1129
	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	Measured	Divided		8852.4	7572.88	1.16896
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Rooted			31.7569	27.9904	1.13456
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Squared			3088.94	4269.96	1.38234
	succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial precursor (cybs) (succinate-ubiquinone reductase membrane anchor subunit) (qps2) (cii-4) (succinate dehydrogenase complex subunit d) (succinate-ubiquinone oxidoreductase cytochrome b small subunit). [swissprot;acc:o14521]	Measured	Subtracted		10	156	146
	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	Ranked	Divided		12196.2	11009.7	1.10777
	transforming protein n-ras. [swissprot;acc:p01111]	Measured		1	16069.8	12885.6	1.24711
	tyrosine-protein kinase hck (ec 2.7.1.112) (p59-hck/p60-hck) (hemopoietic cell kinase). [swissprot;acc:p08631]		Subtracted		6417.18	7859.6	1442.42
220	brain protein 44. [swissprot;acc:o95563]	Rooted			113.374	123.463	10.089
	crk-like protein. [swissprot;acc:p46109]	Measured			6417.18	7859.6	1442.42
	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9]	Squared	Divided		86600.9	65229.9	1.32763
	isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252]	Measured	Subtracted	0	326.677	472.605	145.928
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]		Divided	1	41482.5	33356.5	1.24361
	metastasis-associated protein mta1. [swissprot;acc:q13330]	Rooted			52.7557	60.035	1.13798
	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Ranked	Subtracted		242.339	266.986	24.647
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]		Divided		112	126	1.125
	neurocalcin delta. [swissprot;acc:p29554]			0	13973.6	15473.5	1.10734
	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]		Subtracted		5677.58	4549.85	1127.73
	pnas-18. [sptrembl;acc:q9bzu3]	Rooted			24.2086	21.6857	2.5229
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]		Divided		24.1656	21.3198	1.13348
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Squared	Subtracted		952.068	697.024	255.044
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]		Divided		19892.6	27221.2	1.36841
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Measured			18704	21730	1.16178
	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	Squared	Subtracted	1	57808.9	46630.3	11178.6
221	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]			0	1742.44	1500.84	241.6
	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]		Divided		1614.86	1181.19	1.36715
	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	Measured		1	41482.5	33356.5	1.24361
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Ranked		0	12190.3	13497.2	1.10721
	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]		Subtracted		5677.45	4550.87	1126.58
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Squared	Divided	1	70739	93908.8	1.32754
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Measured	Subtracted	0	1225.09	1079.36	145.73
	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	Ranked	Divided	1	112	126	1.125
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]		Subtracted		242.627	267.151	24.524

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.