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 3730 in total

Filtered  : 0
Value Type  : Ranked
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]	169	11256.8	1.13988	9875.43
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	345	12151.8	1.05086	11563.7
aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	479	15031.7	1.00826	15155.8
alpha crystallin a chain. [swissprot;acc:p02489]	139	13972.2	1.17178	16372.4
alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	421	10866.3	1.02942	11186
alpha-nac protein. [sptrembl;acc:q9h009]	390	14724.5	1.03662	14204.4
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	133	8009	1.17537	6814
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	279	9812.39	1.08171	10614.2
apoptosis inhibitor fksg2. [swissprot;acc:q9hau6]	427	11582.7	1.02719	11276.1
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]	118	14370.7	1.19269	12049
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	52	4554.5	1.38688	3284
arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]	449	9690.83	1.02129	9897.12
arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]	264	10935.1	1.08947	10037.1
aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	466	1521	1.01446	1543
associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799]	278	10763.4	1.08181	11644
ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]	74	8759.5	1.29915	6742.5
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	476	8329	1.00888	8403
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	224	8889.93	1.10413	9815.6
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]	426	9676.67	1.02805	9412.67
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	307	1021	1.06856	1091
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	464	9928.08	1.01494	10076.4
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	24	8257	1.66289	13730.5
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392]	217	6406.18	1.10858	7101.79
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	117	13771.5	1.19285	11545
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	30	11625	1.57201	7395
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]	237	9067	1.10114	9984
block 23. [sptrembl;acc:q8nhw5]	149	13334.8	1.16265	11469.3
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	418	17180.3	1.02995	16680.7
	420	17183	1.02991	16684
blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161]	419
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	114	10603.2	1.19525	8871.11
bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	91	11127.5	1.24387	13841.2
brain protein 16. [refseq;acc:nm_016458]	49	4854.99	1.41927	6890.54
brca1 associated protein. [refseq;acc:nm_006768]	502	0.00001	1	0.00001
bystin. [swissprot;acc:q13895]	384	11244.5	1.03796	10833.3
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	208	10638.4	1.11354	11846.3
cab2. [refseq;acc:nm_033419]	7	10950	1.99689	21866
calcyphosine. [swissprot;acc:q13938]	374	9478.1	1.04183	9874.54
camp-dependent protein kinase, gamma-catalytic subunit (ec 2.7.1.37) (pka c-gamma). [swissprot;acc:p22612]	300	8650.24	1.0717	9270.49
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	347	7311	1.0491	7670
cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	50	13091.4	1.41533	9249.73
casein kinase i alpha s-like. [refseq;acc:nm_145203]	343	8788.62	1.05173	8356.31
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	160	13530.6	1.15331	11732
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]	451	13737.2	1.01987	14010.2
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	245	13019	1.09702	11867.6
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	38	10771	1.48976	7230
chromodomain y-like protein 2. [refseq;acc:nm_152342]	383	10665.1	1.03816	10273.1
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	314	10957.5	1.06369	10301.4
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	275	11674.1	1.08264	10783
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	428	12301.2	1.02658	11982.7

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.