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

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Showing element 577 to 626 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
289	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	Divided	246.892	272.781	1.10486
	syntaxin 6. [swissprot;acc:o43752]	Subtracted	257.414	234.673	22.741
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	Divided	210.064	231.969	1.10428
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Subtracted	264.79	242.109	22.681
291	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]		264.163	241.509	22.654
	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	Divided	228.037	251.679	1.10368
292	40s ribosomal protein s15a. [swissprot;acc:p39027]		266.414	241.411	1.10357
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	Subtracted	256.627	234.146	22.481
293	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Divided	265.717	240.782	1.10356
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Subtracted	196.978	219.421	22.443
294	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]	Divided	265.717	240.782	1.10356
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Subtracted	196.978	219.421	22.443
295	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]
	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	Divided	202.423	223.273	1.103
296	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Subtracted	196.978	219.421	22.443
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	Divided	266.12	241.282	1.10294
297	60s ribosomal protein l7. [swissprot;acc:p18124]		259.984	235.727	1.1029
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Subtracted	196.978	219.421	22.443
298	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	Divided	243.588	268.632	1.10281
	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Subtracted	244.236	266.421	22.185
299	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	Divided	243.592	268.635	1.10281
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Subtracted	244.236	266.421	22.185
300	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Divided	166.351	150.959	1.10196
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Subtracted	234.945	257.017	22.072
301	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Divided	166.372	150.982	1.10193
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Subtracted	110.265	88.2482	22.0168
302	60s ribosomal protein l26. [swissprot;acc:q02877]	Divided	267.008	242.326	1.10185
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Subtracted	110.265	88.2482	22.0168
303	60s ribosomal protein l35. [swissprot;acc:p42766]	Divided	266.999	242.333	1.10179
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Subtracted	110.265	88.2482	22.0168
304	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Divided	266.986	242.339	1.1017
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Subtracted	110.265	88.2482	22.0168
305	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Divided	266.986	242.339	1.1017
306	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		266.673	242.153	1.10126
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Subtracted	110.265	88.2482	22.0168
307	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Divided	266.673	242.153	1.10126
308	60s ribosomal protein l34. [swissprot;acc:p49207]
	necdin. [swissprot;acc:q99608]	Subtracted	110.265	88.2482	22.0168
309	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Divided	266.673	242.153	1.10126
310	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Subtracted	110.265	88.2482	22.0168
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Divided	266.673	242.153	1.10126
311	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Subtracted	110.265	88.2482	22.0168
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Divided	267.151	242.627	1.10108
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]		266.663	242.195	1.10103
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Subtracted	110.265	88.2482	22.0168
313	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Divided	211.207	232.473	1.10069

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.