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 4508 to 4557 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2254	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Subtracted	4632.65	4892.66	260.01
2255	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Divided	3624.59	3463.37	1.04655
	m-phase inducer phosphatase 2 (ec 3.1.3.48) (dual specificity phosphatase cdc25b). [swissprot;acc:p30305]	Subtracted	4383.34	4642.93	259.59
2256	early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566]		4871.11	5129.63	258.52
	ubiquitin. [swissprot;acc:p02248]	Divided	7390.36	7733.85	1.04648
2257	sr rich protein. [refseq;acc:nm_032870]		6245.32	6534.23	1.04626
	visinin-like protein 3 (vilip-3) (calcium-binding protein bdr-1) (hlp2) (hippocalcin-like protein 1). [swissprot;acc:p37235]	Subtracted	5259.97	5518.26	258.29
2258	60s acidic ribosomal protein p0 (l10e). [swissprot;acc:p05388]	Divided	5150.31	5388.05	1.04616
	neuron specific calcium-binding protein hippocalcin (p23k) (calcium- binding protein bdr-2). [swissprot;acc:p32076]	Subtracted	5259.1	5517.22	258.12
2259	neurocalcin delta. [swissprot;acc:p29554]		5258.96	5517.06	258.1
	ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554]	Divided	6486.84	6786.23	1.04615
2260	block 23. [sptrembl;acc:q8nhw5]		5150.14	5387.84
	palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [swissprot;acc:q9umr5]	Subtracted	3687.37	3429.37	258
2261	38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]	Divided	6486.84	6786.23	1.04615
	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Subtracted	3688.8	3431.33	257.47
2262	fas apoptotic inhibitory molecule. [refseq;acc:nm_018147]		5666.91	5923.48	256.57
	similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9]	Divided	5148.88	5386.34	1.04612
2263	40s ribosomal protein s3a. [swissprot;acc:p49241]		4918.64	5145.39	1.0461
	lipoate-protein ligase, mitochondrial precursor (ec 6.-.-.-) (lipoate biosynthesis protein) (lipoyl ligase) (lipoyltransferase). [swissprot;acc:q9y234]	Subtracted	6327.14	6579.38	252.24
2264	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Divided	3633.74	3473.68	1.04608
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Subtracted	6327.14	6579.38	252.24
2265	defender against cell death 1 (dad-1). [swissprot;acc:p46966]
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	Divided	3612.45	3453.39	1.04606
2266	t-complex 11. [refseq;acc:nm_018679]	Subtracted	6327.14	6579.38	252.24
	transcription factor iib. [refseq;acc:nm_013242]	Divided	9146.11	8743.98	1.04599
2267	splicing factor, arginine/serine-rich 8 (suppressor of white apricot protein homolog). [swissprot;acc:q12872]
	tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3]	Subtracted	6327.14	6579.38	252.24
2268	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]		5285.03	5033.55	251.48
	eyes absent homolog 1. [swissprot;acc:q99502]	Divided	5785.08	6051.03	1.04597
2269	phosducin-like protein (phlp). [swissprot;acc:q13371]	Subtracted	5285.38	5034.86	250.52
	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]	Divided	6373.94	6666.87	1.04596
2270	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]		6568.41	6869.9	1.0459
	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]	Subtracted	5285.38	5034.86	250.52
2271	blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	Divided	6568.51	6869.97	1.04589
	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	Subtracted	5285.38	5034.86	250.52
2272	blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	Divided	6568.51	6869.97	1.04589
	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]	Subtracted	5285.38	5034.86	250.52
2273	dna repair protein rad52 homolog. [swissprot;acc:p43351]
	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	Divided	6374.64	6667.06	1.04587
2274	eyes absent homolog 3. [swissprot;acc:q99504]		5779.66	6044.78
	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	Subtracted	4915.05	5164.75	249.7
2275	rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175]		5076.73	5326.29	249.56
	transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544]	Divided	6570.74	6872.1	1.04586
2276	cytochrome c. [swissprot;acc:p00001]	Subtracted	5076.73	5326.29	249.56
	sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467]	Divided	5783.69	6048.87	1.04585
2277	heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174]	Subtracted	5076.73	5326.29	249.56
	sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9]	Divided	5783.72	6048.9	1.04585
2278	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]		5783.76	6048.94
	heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807]	Subtracted	5076.73	5326.29	249.56
2279	fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306]

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.