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

Results: HTML CSV LaTeX

Showing element 332 to 381 of 3228 in total

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

Rank	description	red	green	network_comparison
332	neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8]	312	284	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	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
360	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	243.072	266.559	1.09663
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	242.83	266.248	1.09644
362	apical-like protein (apxl protein). [swissprot;acc:q13796]	231.492	211.136	1.09641
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	231.481	211.131	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]	243.208	266.617	1.09625
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	242.744	266.07	1.09609
366	40s ribosomal protein s5. [swissprot;acc:p46782]	242.473	265.756	1.09602
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	234.146	256.627	1.09601
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	242.66	265.715	1.09501
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	242.159	265.104	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]	186.52	170.42	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]	242.37	265.255	1.09442
374	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	267.208	244.168	1.09436
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	242.686	265.516	1.09407
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	257.017	234.945	1.09395
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	242.691	265.481	1.09391
378	60s ribosomal protein l30. [swissprot;acc:p04645]	242.593	265.365	1.09387
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	241.509	264.163	1.0938
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109	264.79	1.09368
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	200.586	183.423	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.