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 5308 to 5357 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2654	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
	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	Divided	4191.15	4226.86	1.00852
2657	dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9]	Subtracted	4000.73	3947.54	53.19
	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	Divided	5327.58	5371.47	1.00824
2658	b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]		8278.73	8211.05
	ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183]	Subtracted	3640.58	3688.96	48.38
2659	mct-1 protein. [refseq;acc:nm_014060]		4778.28	4732.13	46.15
	nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838]	Divided	8277.7	8210.29	1.00821
2660	mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]	Subtracted	4778.28	4732.13	46.15
	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]	Divided	8277.6	8210.21	1.00821
2661	nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653]		8277.66	8210.26
	sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7]	Subtracted	5327.58	5371.47	43.89
2662	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]		7780.98	7741.14	39.84
	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	Divided	4300.46	4334.66	1.00795
2663	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]		4608.54	4576.35	1.00703
	sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864]	Subtracted	7780.98	7741.14	39.84
2664	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	Divided	4608.91	4576.78	1.00702
	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]	Subtracted	7780.98	7741.14	39.84
2665	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	Divided	8936.97	8999.55	1.007
	atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]	Subtracted	7780.98	7741.14	39.84
2666	dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	Divided	4591.08	4621.88	1.00671
	lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]	Subtracted	7780.98	7741.14	39.84
2667	dna-directed rna polymerase ii 7.6 kda polypeptide (ec 2.7.7.6) (rpb10) (rpb7.6) (rpabc5). [swissprot;acc:p52436]	Divided	4071.9	4099.01	1.00666
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Subtracted	7780.98	7741.14	39.84
2668	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]	Divided	8222.61	8169.38	1.00652
	ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112]	Subtracted	7350.69	7390.45	39.76
2669	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Divided	4336.58	4310.3	1.0061
	zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596]	Subtracted	4191.15	4226.86	35.71
2670	creatine kinase, sarcomeric mitochondrial precursor (ec 2.7.3.2) (s- mtck) (mib-ck) (basic-type mitochondrial creatine kinase). [swissprot;acc:p17540]		8971.66	9006.92	35.26
	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	Divided	4336.62	4310.35	1.00609
2671	creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	Subtracted	8972.87	9007.71	34.84
	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	Divided	4338.79	4313.52	1.00586
2672	dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715]	Subtracted	3377.01	3411.47	34.46
	ubiquitin-specific protease otubain 2. [refseq;acc:nm_023112]	Divided	7350.69	7390.45	1.00541
2673	60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]		7780.98	7741.14	1.00515
	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	Subtracted	4300.46	4334.66	34.2
2674	creatine kinase, m chain (ec 2.7.3.2) (m-ck). [swissprot;acc:p06732]		8980.12	9013.33	33.21
	sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864]	Divided	7780.98	7741.14	1.00515
2675	clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]
	peptidyl prolyl isomerase h; cyclophilin h. [refseq;acc:nm_006347]	Subtracted	8979.61	9012.31	32.7
2676	atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]	Divided	7780.98	7741.14	1.00515
	prp18 pre-mrna processing factor 18 homolog. [refseq;acc:nm_003675]	Subtracted	8979.61	9012.31	32.7
2677	j domain protein c21orf55. [swissprot;acc:q9nx36]		8979.78	9012.42	32.64
	lysosomal alpha-mannosidase precursor (ec 3.2.1.24) (mannosidase, alpha b) (lysosomal acid alpha-mannosidase) (laman) (mannosidase alpha class 2b member 1). [swissprot;acc:o00754]	Divided	7780.98	7741.14	1.00515
2678	microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2]	Subtracted	4608.54	4576.35	32.19
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Divided	7780.98	7741.14	1.00515
2679	bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001]	Subtracted	4608.91	4576.78	32.13

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.