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

Results: HTML CSV LaTeX

Showing element 332 to 381 of 3228 in total

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

Rank	green	description	red	network_comparison
332	284	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	312	1.09859
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]	243.583	1.0983
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]	235.383	1.09811
341	263.798	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243	1.09805
342	267.21	40s ribosomal protein s20. [swissprot;acc:p17075]	243.5	1.09737
343	265.136	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	241.625	1.0973
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]	242.14	1.09729
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]
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	211.252	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
354	257.442	syntaxin 10 (syn10). [swissprot;acc:o60499]	234.691
355	257.414	syntaxin 6. [swissprot;acc:o43752]	234.673	1.09691
356	266.796	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24	1.09684
357	266.661	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	1.09683
358	266.662	ribosomal protein l10-like protein. [refseq;acc:nm_080746]
359	262.434	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	239.277	1.09678
360	266.559	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	243.072	1.09663
361	266.248	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	242.83	1.09644
362	211.136	apical-like protein (apxl protein). [swissprot;acc:q13796]	231.492	1.09641
363	211.131	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	231.481	1.09639
364	266.617	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	243.208	1.09625
365	266.07	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	242.744	1.09609
366	265.756	40s ribosomal protein s5. [swissprot;acc:p46782]	242.473	1.09602
367	256.627	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	234.146	1.09601
368	265.715	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	242.66	1.09501
369	265.104	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	242.159	1.09475
370		nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
371	170.42	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	186.52	1.09447
372		ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
373	265.255	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	242.37	1.09442
374	244.168	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	267.208	1.09436
375	265.516	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	242.686	1.09407
376	234.945	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	257.017	1.09395
377	265.481	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	242.691	1.09391
378	265.365	60s ribosomal protein l30. [swissprot;acc:p04645]	242.593	1.09387
379	264.163	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	241.509	1.0938
380	264.79	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109	1.09368
381	183.423	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	200.586	1.09357

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.