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

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Showing element 368 to 417 of 3228 in total

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

Rank	description	network_comparison	green	red
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	1.09501	265.715	242.66
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	1.09475	265.104	242.159
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	170.42	186.52
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	265.255	242.37
374	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	1.09436	244.168	267.208
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	1.09407	265.516	242.686
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	1.09395	234.945	257.017
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	265.481	242.691
378	60s ribosomal protein l30. [swissprot;acc:p04645]	1.09387	265.365	242.593
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	1.0938	264.163	241.509
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	1.09368	264.79	242.109
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	1.09357	183.423	200.586
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	183.66	200.791
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	1.09242	217.739	237.862
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	244.236	266.421
385	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
386	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	1.09029	264.11	242.238
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	208.756	227.575
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	263.62	241.828
391	40s ribosomal protein s16. [swissprot;acc:p17008]
392	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	1.09008	263.615	241.83
393	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	1.09005	207.072	225.719
394	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	1.08948	238.407	218.827
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	262.34	240.801
397	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	1.08932	101.613	110.689
398	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	1.0893	238.358	218.818
399	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	1.08821	226.226	207.889
400	phosducin-like protein (phlp). [swissprot;acc:q13371]	1.08807	226.218	207.908
401	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]
402	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]
403	phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]
404	dna repair protein rad52 homolog. [swissprot;acc:p43351]
405	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	1.0879	226.209	207.931
406	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	1.08731	244.304	265.634
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	1.08673	260.544	239.75
408	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	1.08649	234.804	255.112
409	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	1.08641	261.874	241.045
410	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	1.0864	253.539	233.376
411	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]
412	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	1.08567	261.416	240.788
413	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	1.08525	261.45	240.913
414	katanin p60 subunit a 1. [refseq;acc:nm_007044]	1.08522	252.238	232.431
415	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	1.08514	252.166	232.382
416	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	1.08496	261.041	240.6
417	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	1.08417	253.197	233.539

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.