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	Value Type	green	Interaction Map	description	network_comparison	red	Filtered

Results: HTML CSV LaTeX

Showing element 300 to 349 of 3228 in total

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

Rank	green	description	network_comparison	red
300	166.351	metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889]	1.10196	150.959
301	166.372	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]	1.10193	150.982
302	267.008	60s ribosomal protein l26. [swissprot;acc:q02877]	1.10185	242.326
303	266.999	60s ribosomal protein l35. [swissprot;acc:p42766]	1.10179	242.333
304	266.986	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]	1.1017	242.339
305		mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]
306	266.673	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	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	267.151	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	1.10108	242.627
312	266.663	60s ribosomal protein l3-like. [swissprot;acc:q92901]	1.10103	242.195
313	211.207	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	1.10069	232.473
314	268.604	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	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	267.017	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	1.10022	242.694
317	204.044	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	1.09998	224.445
318	266.18	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	1.09987	242.011
319	264.729	60s ribosomal protein l19. [swissprot;acc:p14118]	1.09969	240.73
320	265.96	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	1.0995	241.892
321	265.959	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	1.09949
322	78.8995	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	1.09948	86.7483
323	265.945	60s ribosomal protein l23a. [swissprot;acc:p29316]	1.09947	241.884
324	268.195	40s ribosomal protein s23. [swissprot;acc:p39028]	1.09941	243.944
325		28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
326	265.924	60s ribosomal protein l5. [swissprot;acc:p46777]	1.09932	241.899
327	267.962	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	1.09903	243.817
328	235.183	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	1.09888	258.437
329	284	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	1.09859	312
330		chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]
331		doc-1 related protein (doc-1r). [swissprot;acc:o75956]
332		neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]
333		neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562]
334		neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]
335		chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]
336		cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]
337	267.527	60s ribosomal protein l12. [swissprot;acc:p30050]	1.0983	243.583
338	267.528	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]
339	267.527	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]
340	258.476	myelin gene expression factor 2. [refseq;acc:nm_016132]	1.09811	235.383
341	263.798	60s ribosomal protein l9. [swissprot;acc:p32969]	1.09805	240.243
342	267.21	40s ribosomal protein s20. [swissprot;acc:p17075]	1.09737	243.5
343	265.136	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	1.0973	241.625
344		40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
345	265.697	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	1.09729	242.14
346	265.119	40s ribosomal protein s3. [swissprot;acc:p23396]		241.612
347	265.697	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]		242.14
348	265.696	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	1.09728
349		surfeit locus protein 5. [swissprot;acc:q15528]

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.