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	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 325 to 374 of 3228 in total

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

Rank	description	green	red	network_comparison
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	268.195	243.944	1.09941
326	60s ribosomal protein l5. [swissprot;acc:p46777]	265.924	241.899	1.09932
327	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	267.962	243.817	1.09903
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	235.183	258.437	1.09888
329	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	284	312	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]	267.527	243.583	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]	258.476	235.383	1.09811
341	60s ribosomal protein l9. [swissprot;acc:p32969]	263.798	240.243	1.09805
342	40s ribosomal protein s20. [swissprot;acc:p17075]	267.21	243.5	1.09737
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	265.136	241.625	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]	265.697	242.14	1.09729
346	40s ribosomal protein s3. [swissprot;acc:p23396]	265.119	241.612
347	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	265.697	242.14
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]	211.252	231.73	1.09694
354	syntaxin 10 (syn10). [swissprot;acc:o60499]	257.442	234.691
355	syntaxin 6. [swissprot;acc:o43752]	257.414	234.673	1.09691
356	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	266.796	243.24	1.09684
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	266.661	243.12	1.09683
358	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	266.662
359	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	262.434	239.277	1.09678
360	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	266.559	243.072	1.09663
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	266.248	242.83	1.09644
362	apical-like protein (apxl protein). [swissprot;acc:q13796]	211.136	231.492	1.09641
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	211.131	231.481	1.09639
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	266.617	243.208	1.09625
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	266.07	242.744	1.09609
366	40s ribosomal protein s5. [swissprot;acc:p46782]	265.756	242.473	1.09602
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	256.627	234.146	1.09601
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	265.715	242.66	1.09501
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	265.104	242.159	1.09475
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	170.42	186.52	1.09447
372	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	265.255	242.37	1.09442
374	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	244.168	267.208	1.09436

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.