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

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Showing element 51 to 100 of 3228 in total

Hugo  : no value
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

description	Rank	red	green	network_comparison
atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	149	142	170	1.19718
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]	2727	221.001	220.927	1.00033
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	2148	217.871	219.366	1.00686
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	452	224.161	207.972	1.07784
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	1568	221.128	224.767	1.01646
basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	2715	216.018	215.903	1.00053
beta-carotene dioxygenase 2; putative b,b-carotene-9',10'-dioxygenase. [refseq;acc:nm_031938]	2221	221.509	220.108	1.00637
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]	271	241.373	267.352	1.10763
block 23. [sptrembl;acc:q8nhw5]	1091	226.205	232.858	1.02941
blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577]	1930	196.964	198.935	1.01001
	1932	196.965	198.936
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	1748	215.673	212.971	1.01269
brain protein 16. [refseq;acc:nm_016458]	1847	216.811	219.195	1.011
c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	321	241.892	265.959	1.09949
calmodulin. [swissprot;acc:p02593]	2928	0.00001	0.00001	1
casein kinase i, epsilon isoform (ec 2.7.1.-) (cki-epsilon) (ckie). [swissprot;acc:p49674]	1710	227.225	224.21	1.01345
casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]	936	232.473	224.372	1.03611
cbf1 interacting corepressor. [refseq;acc:nm_004882]	572	227.86	213.945	1.06504
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	3226	0.00001	0.00001	1
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	832	231.734	222.222	1.0428
collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	1990	219.26	217.194	1.00951
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532]	1938	198.293	196.341	1.00994
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	1452	160.381	163.554	1.01978
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	1423	221.152	216.659	1.02074
cytokine-like nuclear factor n-pac. [refseq;acc:nm_032569]	1170	219.399	213.784	1.02626
cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452]	797	224.244	234.511	1.04578
dc11 protein. [refseq;acc:nm_020186]	2489	194.527	195.08	1.00284
dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	1385	218.47	213.875	1.02148
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]	634	226.523	213.786	1.05958
dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	1591	225.119	228.769	1.01621
dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	1009	229.116	221.823	1.03288
disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	708	220.438	209.118	1.05413
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	724	244.842	232.577	1.05274
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	776	225.996	215.535	1.04854
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	576	235.18	250.419	1.0648
dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	2621	224.891	225.195	1.00135
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0]	2408	194.407	193.706	1.00362
dj681n20.2 (novel protein similar to ferritin, light polypeptide (ftl)). [sptrembl;acc:q9byw6]	700	220.438	209.118	1.05413
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5]	1125	204.404	210.022	1.02748
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	1881	210.592	208.355	1.01074
dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	1329	218.509	213.648	1.02275
dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	339	243.583	267.527	1.0983
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]	906	230.764	239.62	1.03838
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]	905	230.768	239.632	1.03841
dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	1790	203.759	201.349	1.01197
dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	1071	231.277	238.356	1.03061
dok-like protein. [refseq;acc:nm_024872]	653	216.504	204.622	1.05807
dpy-30-like protein. [swissprot;acc:q9c005]	1815	220.462	217.926	1.01164
dystrophin. [swissprot;acc:p11532]	2584	213.422	213.75	1.00154
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	1791	217.866	215.295	1.01194

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
- Hugo is the HGNC identifier if it exists
- 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.