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

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Showing element 268 to 317 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	green	network_comparison	red
268	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	244.167	1.10996	271.016
269	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	267.352	1.10763	241.373
270	fad synthetase. [refseq;acc:nm_025207]
271	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]
272	ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214]
273	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [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:o43252]
274	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435]
275	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]
276	60s ribosomal protein l32. [swissprot;acc:p02433]	266.969	1.10716	241.13
277	40s ribosomal protein s29. [swissprot;acc:p30054]	267.642	1.10665	241.849
278	40s ribosomal protein s11. [swissprot;acc:p04643]	267.088	1.10642	241.399
279	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	228.42	1.10605	252.644
280	metastasis-associated protein mta1. [swissprot;acc:q13330]	228.356	1.10578	252.512
281	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	267.335	1.10557	241.808
282	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	228.297	1.10553	252.39
283	60s ribosomal protein l11. [swissprot;acc:p39026]	267.346	1.10552	241.828
284	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	203.235	1.10541	224.657
285	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	203.242	1.10532	224.647
286	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	203.251	1.1052	224.633
287	40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47]	266.079	1.10517	240.758
288	40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750]	266.078
289	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	246.892	1.10486	272.781
290	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	210.064	1.10428	231.969
291	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]	228.037	1.10368	251.679
292	40s ribosomal protein s15a. [swissprot;acc:p39027]	266.414	1.10357	241.411
293	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	265.717	1.10356	240.782
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]
295	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]	202.423	1.103	223.273
296	mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956]	266.12	1.10294	241.282
297	60s ribosomal protein l7. [swissprot;acc:p18124]	259.984	1.1029	235.727
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]	243.588	1.10281	268.632
299	calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384]	243.592		268.635
300	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	166.351	1.10196	150.959
301	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	166.372	1.10193	150.982
302	60s ribosomal protein l26. [swissprot;acc:q02877]	267.008	1.10185	242.326
303	60s ribosomal protein l35. [swissprot;acc:p42766]	266.999	1.10179	242.333
304	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	266.986	1.1017	242.339
305	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]
306	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	266.673	1.10126	242.153
307	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]
308	60s ribosomal protein l34. [swissprot;acc:p49207]
309	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]
311	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	267.151	1.10108	242.627
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]	266.663	1.10103	242.195
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	211.207	1.10069	232.473
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	268.604	1.10027	244.126
315	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]
316	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	267.017	1.10022	242.694
317	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	204.044	1.09998	224.445

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.