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	network_comparison	green

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Showing element 313 to 362 of 3228 in total

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

Rank	description	red	network_comparison	green
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	232.473	1.10069	211.207
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	244.126	1.10027	268.604
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]	242.694	1.10022	267.017
317	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	224.445	1.09998	204.044
318	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	242.011	1.09987	266.18
319	60s ribosomal protein l19. [swissprot;acc:p14118]	240.73	1.09969	264.729
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	241.892	1.0995	265.96
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]		1.09949	265.959
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	86.7483	1.09948	78.8995
323	60s ribosomal protein l23a. [swissprot;acc:p29316]	241.884	1.09947	265.945
324	40s ribosomal protein s23. [swissprot;acc:p39028]	243.944	1.09941	268.195
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
326	60s ribosomal protein l5. [swissprot;acc:p46777]	241.899	1.09932	265.924
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	243.817	1.09903	267.962
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	258.437	1.09888	235.183
329	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	312	1.09859	284
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	60s ribosomal protein l12. [swissprot;acc:p30050]	243.583	1.0983	267.527
338	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]			267.528
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]			267.527
340	myelin gene expression factor 2. [refseq;acc:nm_016132]	235.383	1.09811	258.476
341	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243	1.09805	263.798
342	40s ribosomal protein s20. [swissprot;acc:p17075]	243.5	1.09737	267.21
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	241.625	1.0973	265.136
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
345	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	242.14	1.09729	265.697
346	40s ribosomal protein s3. [swissprot;acc:p23396]	241.612		265.119
347	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	242.14		265.697
348	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]		1.09728	265.696
349	surfeit locus protein 5. [swissprot;acc:q15528]
350	zinc finger protein 291. [swissprot;acc:q9by12]
351	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
352	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]
353	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	231.73	1.09694	211.252
354	syntaxin 10 (syn10). [swissprot;acc:o60499]	234.691		257.442
355	syntaxin 6. [swissprot;acc:o43752]	234.673	1.09691	257.414
356	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24	1.09684	266.796
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	1.09683	266.661
358	ribosomal protein l10-like protein. [refseq;acc:nm_080746]			266.662
359	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	239.277	1.09678	262.434
360	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	243.072	1.09663	266.559
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	242.83	1.09644	266.248
362	apical-like protein (apxl protein). [swissprot;acc:q13796]	231.492	1.09641	211.136

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.