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

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Showing element 1 to 50 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Hugo  : no value
Interaction Map  : High confidence
Filtered  : 1

Rank	green	network_comparison	description	red
2	28	1.86667	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]	15
30	243.678	1.29991	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	187.457
41	253	1.27273	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	322
43	160.957	1.2714	jun dimerization protein. [refseq;acc:nm_130469]	204.641
56	336.233	1.25998	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	266.856
63	336.178	1.25973	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	266.865
85	110.265	1.24949	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	88.2482
88			hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]
94			melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]
99			melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]
147	42.3003	1.2009	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	50.7983
149	170	1.19718	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	142
152	46	1.19565	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	55
168	98.0548	1.18722	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	82.5916
178	194.72	1.1652	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	226.887
179	194.79	1.16476	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	226.884
191	198.444	1.14179	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	226.582
215	126	1.125	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	112
221			myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
238	254.15	1.11785	rd protein. [swissprot;acc:p18615]	227.357
247	212.41	1.11719	rna-binding protein. [refseq;acc:nm_019027]	237.302
248			apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
271	267.352	1.10763	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	241.373
277	267.642	1.10665	40s ribosomal protein s29. [swissprot;acc:p30054]	241.849
281	267.335	1.10557	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	241.808
288	266.078	1.10517	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	240.758
289	246.892	1.10486	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	272.781
293	265.717	1.10356	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	240.782
297	259.984	1.1029	60s ribosomal protein l7. [swissprot;acc:p18124]	235.727
304	266.986	1.1017	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	242.339
306	266.673	1.10126	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	242.153
317	204.044	1.09998	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	224.445
321	265.959	1.09949	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	241.892
323	265.945	1.09947	60s ribosomal protein l23a. [swissprot;acc:p29316]	241.884
337	267.527	1.0983	60s ribosomal protein l12. [swissprot;acc:p30050]	243.583
338	267.528		60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]
339	267.527		dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]
341	263.798	1.09805	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243
344	265.136	1.0973	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	241.625
348	265.696	1.09728	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	242.14
356	266.796	1.09684	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24
357	266.661	1.09683	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12
372	170.42	1.09447	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	186.52
380	264.79	1.09368	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109
387	264.11	1.09029	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	242.238
388	208.756	1.09015	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	227.575
396	262.34	1.08945	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	240.801
406	244.304	1.08731	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	265.634
410	253.539	1.0864	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	233.376
452	207.972	1.07784	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	224.161

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
- Hugo is the HGNC identifier if it exists
- 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.