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

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Showing element 1 to 50 of 3228 in total

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

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

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.