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

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Showing element 101 to 150 of 3730 in total

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

description	Rank	red	network_comparison	green
coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	372	5427.25	1.05782	5130.58
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	345	2113.27	1.0672	2255.28
cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	456	17356	1.01343	17126
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	257	861.401	1.13358	759.896
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	202	606.049	1.19421	723.75
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	14	130.512	20.0687	6.50325
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	299	2231.05	1.10717	2015.09
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	175	1382.5	1.24887	1107
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	162	5734.28	1.26468	7252.02
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	166	5629.62	1.2611	7099.51
cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6]	147	292.152	1.29455	378.206
cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2]	146	291.639	1.29466	377.574
cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329]	149	293.178	1.29435	379.474
cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187]	148
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	132	42	1.33333	56
daz associated protein 1 isoform b; deleted in azoospermia associated protein 1. [refseq;acc:nm_018959]	114	671.769	1.4204	472.945
dc11 protein. [refseq;acc:nm_020186]	180	556	1.22482	681
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	327	175.644	1.09034	161.091
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	109	100	1.44	144
dead-box protein. [refseq;acc:nm_018665]	76	313.667	1.71403	183
dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]	476	1362.55	1.00716	1372.31
deltex homolog 1; hdx-1. [refseq;acc:nm_004416]	48	870.482	2.15895	403.196
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	463	1262.65	1.01163	1248.14
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	200	578.056	1.19755	482.7
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513]	321	628.072	1.09333	686.693
dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	197	2145.97	1.20275	1784.22
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	62	210.767	1.82385	384.407
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	277	870.93	1.12024	975.647
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	473	3889.5	1.00765	3919.25
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	450	4158.33	1.01569	4094.09
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	285	2698.62	1.11547	3010.22
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	336	1766.66	1.08008	1908.13
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	69	1593	1.7602	2804
dj579f20.1 (high-mobility group (nonhistone chromosomal) protein 1-like 1). [sptrembl;acc:q9nqj4]	489	22946.3	1.00224	22895.1
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	93	528.5	1.54494	816.5
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	229	320.752	1.14829	368.317
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	52	999.28	2.07438	481.725
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	387	1388.29	1.04354	1330.37
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	178	498.07	1.23523	615.233
dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	174	488.43	1.25423	612.604
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	329	1658.07	1.08883	1805.36
dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	369	1048.65	1.06044	988.882
dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	370	1049.21	1.06041	989.438
dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	457	1562.36	1.01341	1541.69
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	290	1370.82	1.11288	1525.56
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	461	1915.69	1.01229	1892.44
dok-like protein. [refseq;acc:nm_024872]	31	35	3500000	0.00001
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832]	312	3455.43	1.0998	3800.29
dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	340	559.333	1.07271	600
dystrophin. [swissprot;acc:p11532]	30	427.217	3.82335	111.739

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.