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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Gene	Rank	description	Value Type	red	Network Comparison Type	Interaction Map	network_comparison	Filtered	green

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Showing element 16530 to 16579 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	Network Comparison Type	network_comparison	green
2067	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Measured	3602.75	Divided	1.05616	3411.18
	adenylosuccinate lyase (ec 4.3.2.2) (adenylosuccinase) (asl) (asase). [swissprot;acc:p30566]	Ranked	193.226		1.00828	191.639
	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]		207.655	Subtracted	1.716	205.939
	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]	Rooted	59.3823		1.6271	61.0094
	conserved oligomeric golgi complex component 6. [swissprot;acc:q9y2v7]		66.6886	Divided	1.02621	68.4366
	rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	Squared	15001.4	Subtracted	1950.1	16951.5
	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]		24225.6	Divided	1.08972	26399
2068	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
	bystin. [swissprot;acc:q13895]		16837.1	Subtracted	1949	18786.1
	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]	Ranked	220.8	Divided	1.0082	222.61
	hyaluronan synthase 2 (ec 2.4.1.212) (hyaluronate synthase 2) (hyaluronic acid synthase 2) (ha synthase 2). [swissprot;acc:q92819]	Measured	5391.27	Subtracted	315.37	5706.64
	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]		3602.75	Divided	1.05616	3411.17
	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	Ranked	207.638	Subtracted	1.715	205.923
	ring finger protein 40; 95 kda retinoblastoma protein binding protein; likely ortholog of rat staring. [refseq;acc:nm_014771]	Rooted	59.5914	Divided	1.02621	61.1533
	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]		59.3823	Subtracted	1.6271	61.0094
2069	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742]	Squared	23062.1		1943	25005.1
	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Measured	4632.65	Divided	1.05613	4892.66
	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	Ranked	217.555		1.0081	215.807
	fidgetin-like 1. [refseq;acc:nm_022116]		215.511	Subtracted	1.697	213.814
	hyaluronan synthase 1 (ec 2.4.1.212) (hyaluronate synthase 1) (hyaluronic acid synthase 1) (ha synthase 1) (huhas1). [swissprot;acc:q92839]	Measured	5391.27		315.37	5706.64
	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	Rooted	55.9946	Divided	1.0262	57.4614
	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]	Squared	24225.6		1.08972	26399
		Rooted	59.3823	Subtracted	1.6271	61.0094
2070	actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]	Squared	24225.6	Divided	1.08972	26399
		Rooted	59.3823	Subtracted	1.6271	61.0094
	hyaluronan synthase 3 (ec 2.4.1.212) (hyaluronate synthase 3) (hyaluronic acid synthase 3) (ha synthase 3). [swissprot;acc:o00219]	Measured	5391.27		315.37	5706.64
	maguk p55 subfamily member 3 (mpp3 protein) (discs, large homolog 3). [swissprot;acc:q13368]	Ranked	218.124		1.691	216.433
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Squared	16038		1935.3	17973.3
	polybromo 1. [refseq;acc:nm_018165]	Rooted	61.089	Divided	1.02615	62.6862
	rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	Ranked	223.199		1.0081	225.008
	splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246]	Measured	10178.5		1.05607	9638.08
2071	28s ribosomal protein s26, mitochondrial precursor (mrp-s26) (mrp- s13). [swissprot;acc:q9byn8]		6437.24		1.05592	6797.24
	adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203]	Ranked	199.928	Subtracted	1.688	198.24
	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]	Squared	24225.6	Divided	1.08972	26399
		Rooted	59.3823	Subtracted	1.6271	61.0094
	fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087]	Squared	15565.5		1935.1	17500.6
	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	Measured	5859.1		314.6	6173.7
	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	Ranked	217.555	Divided	1.0081	215.807
	swi/snf-related matrix-associated actin-dependent regulator of chromatin a5; sucrose nonfermenting-like 5. [refseq;acc:nm_003601]	Rooted	61.089		1.02615	62.6862
2072	dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]	Ranked	217.555		1.0081	215.807
	enhancer of rudimentary homolog. [swissprot;acc:q14259]	Measured	6437.24		1.05592	6797.24
	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]	Squared	24225.6		1.08972	26399
		Rooted	59.3823	Subtracted	1.6271	61.0094
	ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]	Ranked	199.928		1.688	198.24
	oxidation resistance 1. [refseq;acc:nm_181354]	Measured	5859.1		314.6	6173.7
	possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]	Rooted	61.089	Divided	1.02615	62.6862
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Squared	17375.5	Subtracted	1932.6	19308.1
2073	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]		24225.6	Divided	1.08972	26399
		Rooted	59.3823	Subtracted	1.6271	61.0094
	adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]	Ranked	199.928		1.688	198.24

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.