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	network_comparison	Filtered	red	green

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Showing element 351 to 400 of 3228 in total

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

Rank	description	network_comparison	red	green
351	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	1.09728	242.14	265.696
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]	1.09694	231.73	211.252
354	syntaxin 10 (syn10). [swissprot;acc:o60499]		234.691	257.442
355	syntaxin 6. [swissprot;acc:o43752]	1.09691	234.673	257.414
356	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	1.09684	243.24	266.796
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	1.09683	243.12	266.661
358	ribosomal protein l10-like protein. [refseq;acc:nm_080746]			266.662
359	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	1.09678	239.277	262.434
360	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	1.09663	243.072	266.559
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	1.09644	242.83	266.248
362	apical-like protein (apxl protein). [swissprot;acc:q13796]	1.09641	231.492	211.136
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	1.09639	231.481	211.131
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	1.09625	243.208	266.617
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	1.09609	242.744	266.07
366	40s ribosomal protein s5. [swissprot;acc:p46782]	1.09602	242.473	265.756
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	1.09601	234.146	256.627
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	1.09501	242.66	265.715
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	1.09475	242.159	265.104
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]	1.09447	186.52	170.42
372	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	1.09442	242.37	265.255
374	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	1.09436	267.208	244.168
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	1.09407	242.686	265.516
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	1.09395	257.017	234.945
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	1.09391	242.691	265.481
378	60s ribosomal protein l30. [swissprot;acc:p04645]	1.09387	242.593	265.365
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	1.0938	241.509	264.163
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	1.09368	242.109	264.79
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	1.09357	200.586	183.423
382	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	1.09328	200.791	183.66
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	1.09242	237.862	217.739
384	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	1.09083	266.421	244.236
385	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
386	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	1.09029	242.238	264.11
387	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
388	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	1.09015	227.575	208.756
389	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
390	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	1.09011	241.828	263.62
391	40s ribosomal protein s16. [swissprot;acc:p17008]
392	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	1.09008	241.83	263.615
393	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	1.09005	225.719	207.072
394	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	1.08948	218.827	238.407
395	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
396	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	1.08945	240.801	262.34
397	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	1.08932	110.689	101.613
398	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	1.0893	218.818	238.358
399	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	1.08821	207.889	226.226
400	phosducin-like protein (phlp). [swissprot;acc:q13371]	1.08807	207.908	226.218

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.