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

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Showing element 132 to 181 of 3228 in total

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

description	Rank	red	green	network_comparison
60s ribosomal protein l21. [swissprot;acc:p46778]	1054	223.958	217.263	1.03082
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268]	2205	199.129	200.413	1.00645
60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	293	240.782	265.717	1.10356
60s ribosomal protein l23a. [swissprot;acc:p29316]	323	241.884	265.945	1.09947
60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	1767	201.288	198.86	1.01221
60s ribosomal protein l26. [swissprot;acc:q02877]	302	242.326	267.008	1.10185
60s ribosomal protein l28. [swissprot;acc:p46779]	1882	215.896	213.61	1.0107
60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]	2664	204.768	204.549	1.00107
60s ribosomal protein l3-like. [swissprot;acc:q92901]	312	242.195	266.663	1.10103
60s ribosomal protein l30. [swissprot;acc:p04645]	378	242.593	265.365	1.09387
60s ribosomal protein l31. [swissprot;acc:p12947]	862	234.025	224.958	1.04031
60s ribosomal protein l32. [swissprot;acc:p02433]	276	241.13	266.969	1.10716
60s ribosomal protein l34, mitochondrial precursor (l34mt). [swissprot;acc:q9bq48]	1333	220.681	215.78	1.02271
60s ribosomal protein l34. [swissprot;acc:p49207]	308	242.153	266.673	1.10126
60s ribosomal protein l35. [swissprot;acc:p42766]	303	242.333	266.999	1.10179
60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	365	242.744	266.07	1.09609
60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	635	228.639	242.258	1.05957
60s ribosomal protein l37a. [swissprot;acc:p12751]	2959	0.00001	0.00001	1
60s ribosomal protein l39. [swissprot;acc:p02404]	859	234.025	224.958	1.04031
60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	359	239.277	262.434	1.09678
60s ribosomal protein l5. [swissprot;acc:p46777]	326	241.899	265.924	1.09932
60s ribosomal protein l7. [swissprot;acc:p18124]	297	235.727	259.984	1.1029
60s ribosomal protein l8. [swissprot;acc:p25120]	834	231.734	222.222	1.0428
60s ribosomal protein l9. [swissprot;acc:p32969]	341	240.243	263.798	1.09805
65 kda yes-associated protein (yap65). [swissprot;acc:p46937]	1986	219.26	217.193	1.00952
69 kda islet cell autoantigen (ica69) (islet cell autoantigen 1) (islet cell autoantigen p69) (icap69). [swissprot;acc:q05084]	3227	0.00001	0.00001	1
9 kda protein. [swissprot;acc:p13994]	1988	219.26	217.193	1.00952
a kindred of iglon. [refseq;acc:nm_173808]	804	212.386	221.785	1.04425
a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588]	2788	0.00001	0.00001	1
a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	957	129.913	134.399	1.03453
aarf domain containing kinase 1. [refseq;acc:nm_020421]	1733	215.336	212.567	1.01303
aarf domain containing kinase 2; putative ubiquinone biosynthesis protein aarf. [refseq;acc:nm_052853]	1731
aarf domain containing kinase 4. [refseq;acc:nm_024876]	1732
abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910]	1935	218.43	216.279	1.00995
abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759]	1845	217.077	214.702	1.01106
acetyl-coa acetyltransferase, mitochondrial precursor (ec 2.3.1.9) (acetoacetyl-coa thiolase) (t2). [swissprot;acc:p24752]	2306	191.571	192.544	1.00508
acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085]	2319	194.842	195.8	1.00492
acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763]	2315	194.825	195.787	1.00494
acetyl-coenzyme a synthetase, cytoplasmic (ec 6.2.1.1) (acetate--coa ligase) (acyl-activating enzyme) (acetyl-coa synthetase) (acs) (acecs). [swissprot;acc:q9nr19]	2039	190.551	192.191	1.00861
acid ceramidase precursor (ec 3.5.1.23) (acylsphingosine deacylase) (n-acylsphingosine amidohydrolase) (ac) (putative 32 kda heart protein) (php32). [swissprot;acc:q13510]	1421	207.076	211.391	1.02084
acrc protein; putative nuclear protein. [refseq;acc:nm_052957]	2101	211.71	213.27	1.00737
actin binding lim protein 2. [refseq;acc:nm_032432]	660	229.072	216.576	1.0577
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]	1529	216.762	213.031	1.01751
actin-binding lim protein 1 isoform a; lim actin-binding protein 1; limatin; actin-binding lim protein. [refseq;acc:nm_002313]	668	229.072	216.576	1.0577
actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]	2626	224.891	225.195	1.00135
actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]	2631
actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]	2634
activated p21cdc42hs kinase. [refseq;acc:nm_005781]	2341	229.258	230.294	1.00452
activator of basal transcription 1; tata-binding protein-binding protein; basal transcriptional activator. [refseq;acc:nm_013375]	1169	219.399	213.784	1.02626
activator of camp-responsive element modulator (crem) in testis; lim protein act. [refseq;acc:nm_020482]	1303	269.157	275.531	1.02368

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.