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

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Showing element 310 to 359 of 3228 in total

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

Rank	description	red	green	network_comparison
310	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	242.153	266.673	1.10126
311	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	242.627	267.151	1.10108
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]	242.195	266.663	1.10103
313	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	232.473	211.207	1.10069
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	244.126	268.604	1.10027
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	267.017	1.10022
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	204.044	1.09998
318	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	242.011	266.18	1.09987
319	60s ribosomal protein l19. [swissprot;acc:p14118]	240.73	264.729	1.09969
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	241.892	265.96	1.0995
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]		265.959	1.09949
322	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	86.7483	78.8995	1.09948
323	60s ribosomal protein l23a. [swissprot;acc:p29316]	241.884	265.945	1.09947
324	40s ribosomal protein s23. [swissprot;acc:p39028]	243.944	268.195	1.09941
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
326	60s ribosomal protein l5. [swissprot;acc:p46777]	241.899	265.924	1.09932
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	243.817	267.962	1.09903
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	258.437	235.183	1.09888
329	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	312	284	1.09859
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	267.527	1.0983
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	258.476	1.09811
341	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243	263.798	1.09805
342	40s ribosomal protein s20. [swissprot;acc:p17075]	243.5	267.21	1.09737
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	241.625	265.136	1.0973
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	265.697	1.09729
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]		265.696	1.09728
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	211.252	1.09694
354	syntaxin 10 (syn10). [swissprot;acc:o60499]	234.691	257.442
355	syntaxin 6. [swissprot;acc:o43752]	234.673	257.414	1.09691
356	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24	266.796	1.09684
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	266.661	1.09683
358	ribosomal protein l10-like protein. [refseq;acc:nm_080746]		266.662
359	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	239.277	262.434	1.09678

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.