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

Results: HTML CSV LaTeX

Showing element 580 to 629 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
290	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Subtracted	242.109	264.79	22.681
291	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]		241.509	264.163	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	251.679	228.037	1.10368
292	40s ribosomal protein s15a. [swissprot;acc:p39027]		241.411	266.414	1.10357
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	Subtracted	234.146	256.627	22.481
293	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Divided	240.782	265.717	1.10356
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Subtracted	219.421	196.978	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	240.782	265.717	1.10356
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Subtracted	219.421	196.978	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	223.273	202.423	1.103
296	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	Subtracted	219.421	196.978	22.443
	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	Divided	241.282	266.12	1.10294
297	60s ribosomal protein l7. [swissprot;acc:p18124]		235.727	259.984	1.1029
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	Subtracted	219.421	196.978	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	268.632	243.588	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	266.421	244.236	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	268.635	243.592	1.10281
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Subtracted	266.421	244.236	22.185
300	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	Divided	150.959	166.351	1.10196
	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	Subtracted	257.017	234.945	22.072
301	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	Divided	150.982	166.372	1.10193
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Subtracted	88.2482	110.265	22.0168
302	60s ribosomal protein l26. [swissprot;acc:q02877]	Divided	242.326	267.008	1.10185
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Subtracted	88.2482	110.265	22.0168
303	60s ribosomal protein l35. [swissprot;acc:p42766]	Divided	242.333	266.999	1.10179
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Subtracted	88.2482	110.265	22.0168
304	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	Divided	242.339	266.986	1.1017
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Subtracted	88.2482	110.265	22.0168
305	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]
	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	Divided	242.339	266.986	1.1017
306	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		242.153	266.673	1.10126
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Subtracted	88.2482	110.265	22.0168
307	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Divided	242.153	266.673	1.10126
308	60s ribosomal protein l34. [swissprot;acc:p49207]
	necdin. [swissprot;acc:q99608]	Subtracted	88.2482	110.265	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	242.153	266.673	1.10126
310	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Subtracted	88.2482	110.265	22.0168
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Divided	242.153	266.673	1.10126
311	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Subtracted	88.2482	110.265	22.0168
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Divided	242.627	267.151	1.10108
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]		242.195	266.663	1.10103
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	Subtracted	88.2482	110.265	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	232.473	211.207	1.10069
314	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Subtracted	88.2482	110.265	22.0168
	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	Divided	244.126	268.604	1.10027
315	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Subtracted	88.2482	110.265	22.0168

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.