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

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Showing element 51 to 100 of 14920 in total

Filtered  : 0
Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence

description	Rank	green	network_comparison	red
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	452	1504.85	1.01496	1527.36
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	231	1759.22	1.14705	2017.91
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	266	1312.91	1.1235	1475.05
alpha crystallin a chain. [swissprot;acc:p02489]	86	89.2447	1.61366	55.3059
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	475	2335.98	1.00722	2319.24
alpha-nac protein. [sptrembl;acc:q9h009]	436	151.122	1.0265	147.221
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	116	475	1.40632	668
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	332	14167	1.08783	15411.3
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	276	12125.1	1.12092	10817.1
aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	164	1354.26	1.26383	1711.55
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	211	2076.5	1.18661	2464
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	337	2194.52	1.07624	2039.07
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	213	1376.88	1.18471	1162.21
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	441	6303	1.02355	6158
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	139	561.038	1.31317	736.737
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	216	14756	1.18256	12478
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	477	429	1.00704	426
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	377	931.405	1.05332	884.254
atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	100	402	1.47761	594
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	292	12473	1.11138	11223
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	191	904.149	1.21678	743.066
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	9	6410	75.4118	85
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	348	13463.1	1.0664	14357.1
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	108	421	1.44178	292
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	28	139	4.10072	570
bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	133	335	1.32937	252
block 23. [sptrembl;acc:q8nhw5]	293	2159.55	1.11127	1943.32
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	184	306.727	1.22281	375.07
	185	306.933		375.322
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	183	306.727		375.07
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	453	1356.52	1.01438	1337.29
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	74	859.34	1.71473	501.151
brain protein 16. [refseq;acc:nm_016458]	274	2418.14	1.12172	2155.75
brca1 associated protein. [refseq;acc:nm_006768]	502	0.00001	1	0.00001
bystin. [swissprot;acc:q13895]	343	3135.76	1.0699	2930.88
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	261	1463.55	1.12945	1295.81
cab2. [refseq;acc:nm_033419]	2	174	17400000	0.00001
calcyphosine. [swissprot;acc:q13938]	126	635.875	1.3457	472.524
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	381	2633.79	1.04972	2509.05
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	316	576	1.09714	525
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	207	339.154	1.19069	403.827
casein kinase i alpha s-like. [refseq;acc:nm_145203]	238	1933.94	1.13678	2198.47
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	141	891.114	1.30385	1161.88
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	279	610.424	1.11819	545.902
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	319	1268.19	1.09483	1388.45
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	32	184	3.25	598
chromodomain y-like protein 2. [refseq;acc:nm_152342]	326	2799.81	1.09054	3053.31
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	286	6127.24	1.11465	5497.01
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	173	4102.97	1.25656	3265.25
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	226	758.411	1.15165	658.544

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.