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

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Showing element 1 to 50 of 3228 in total

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

Rank	network_comparison	description	red	green
2	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	28
30	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	243.678
41	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	253
43	1.2714	jun dimerization protein. [refseq;acc:nm_130469]	204.641	160.957
56	1.25998	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	266.856	336.233
63	1.25973	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	266.865	336.178
85	1.24949	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	88.2482	110.265
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	1.2009	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	50.7983	42.3003
149	1.19718	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	142	170
152	1.19565	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	55	46
168	1.18722	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	82.5916	98.0548
178	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	194.72
179	1.16476	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	226.884	194.79
191	1.14179	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	226.582	198.444
215	1.125	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	112	126
221		myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]
238	1.11785	rd protein. [swissprot;acc:p18615]	227.357	254.15
247	1.11719	rna-binding protein. [refseq;acc:nm_019027]	237.302	212.41
248		apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
271	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	267.352
277	1.10665	40s ribosomal protein s29. [swissprot;acc:p30054]	241.849	267.642
281	1.10557	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	241.808	267.335
288	1.10517	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	240.758	266.078
289	1.10486	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	272.781	246.892
293	1.10356	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	240.782	265.717
297	1.1029	60s ribosomal protein l7. [swissprot;acc:p18124]	235.727	259.984
304	1.1017	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	242.339	266.986
306	1.10126	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	242.153	266.673
317	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	204.044
321	1.09949	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	241.892	265.959
323	1.09947	60s ribosomal protein l23a. [swissprot;acc:p29316]	241.884	265.945
337	1.0983	60s ribosomal protein l12. [swissprot;acc:p30050]	243.583	267.527
338		60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]		267.528
339		dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]		267.527
341	1.09805	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243	263.798
344	1.0973	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	241.625	265.136
348	1.09728	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	242.14	265.696
356	1.09684	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24	266.796
357	1.09683	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	266.661
372	1.09447	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	186.52	170.42
380	1.09368	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109	264.79
387	1.09029	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	242.238	264.11
388	1.09015	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	227.575	208.756
396	1.08945	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	240.801	262.34
406	1.08731	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	265.634	244.304
410	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	253.539
452	1.07784	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	224.161	207.972

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.