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 682 to 731 of 3730 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	green	network_comparison
341	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	0	8702.94	9169.98	1.05366
342	40s ribosomal protein s20. [swissprot;acc:p17075]	1	243.5	267.21	1.09737
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	0	10074	10609	1.05311
343	casein kinase i alpha s-like. [refseq;acc:nm_145203]		8356.31	8788.62	1.05173
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	1	241.625	265.136	1.0973
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	0	10540.6	10027.6	1.05116
345	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]		11563.7	12151.8	1.05086
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	1	242.14	265.697	1.09729
346	40s ribosomal protein s3. [swissprot;acc:p23396]		241.612	265.119
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	0	9267.81	9736.2	1.05054
347	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]		7670	7311	1.0491
	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	1	242.14	265.697	1.09729
348	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]			265.696	1.09728
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	0	16321	15577	1.04776
349	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]
	surfeit locus protein 5. [swissprot;acc:q15528]	1	242.14	265.696	1.09728
350	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	0	16321	15577	1.04776
	zinc finger protein 291. [swissprot;acc:q9by12]	1	242.14	265.696	1.09728
351	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	0	16321	15577	1.04776
	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	1	242.14	265.696	1.09728
352	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	0	16321	15577	1.04776
	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	1	242.14	265.696	1.09728
353	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	0	16321	15577	1.04776
	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	1	231.73	211.252	1.09694
354	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	0	16321	15577	1.04776
	syntaxin 10 (syn10). [swissprot;acc:o60499]	1	234.691	257.442	1.09694
355	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	0	16321	15577	1.04776
	syntaxin 6. [swissprot;acc:o43752]	1	234.673	257.414	1.09691
356	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]		243.24	266.796	1.09684
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	0	16321	15577	1.04776
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	1	243.12	266.661	1.09683
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	0	16321	15577	1.04776
358	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]
	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	1	243.12	266.662	1.09683
359	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]		239.277	262.434	1.09678
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	0	16321	15577	1.04776
360	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]
	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	1	243.072	266.559	1.09663
361	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	0	16321	15577	1.04776
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	1	242.83	266.248	1.09644
362	apical-like protein (apxl protein). [swissprot;acc:q13796]		231.492	211.136	1.09641
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	0	16321	15577	1.04776
363	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	1	231.481	211.131	1.09639
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]		243.208	266.617	1.09625
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	0	16321	15577	1.04776
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	1	242.744	266.07	1.09609
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	0	7769.96	8139.71	1.04759
366	40s ribosomal protein s5. [swissprot;acc:p46782]	1	242.473	265.756	1.09602

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.