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

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Showing element 651 to 700 of 3228 in total

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

description	Rank	red	green	network_comparison
crk-like protein. [swissprot;acc:p46109]	252	6417.18	7859.6	1.22477
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	366	5189	6088.47	1.17334
ctcl tumor antigen l14-2. [refseq;acc:nm_018017]	2846	0.00001	0.00001	1
ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	748	12503.3	11212	1.11517
cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879]	2182	5875.13	6173.41	1.05077
cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561]	2183	5875.11	6173.39
cullin homolog 1 (cul-1). [swissprot;acc:q13616]	103	2353.63	3225.65	1.3705
cullin homolog 2 (cul-2). [swissprot;acc:q13617]	101
cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336]	1480	5660.17	6085.22	1.07509
cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	78	4800.81	7132.71	1.48573
cyclic-amp-dependent transcription factor atf-6 alpha (activating transcription factor 6 alpha) (atf6-alpha). [swissprot;acc:p18850]	1267	5894.47	6383.73	1.083
cyclic-amp-dependent transcription factor atf-6 beta (activating transcription factor 6 beta) (atf6-beta) (camp responsive element binding protein-like 1) (camp response element binding protein-related protein) (creb-rp) (g13 protein). [swissprot;acc:q99941]	1264
cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544]	1478	5659.22	6084.68	1.07518
cyclin c. [swissprot;acc:p24863]	1353	6200.93	6690.57	1.07896
cyclin g1 (cyclin g). [swissprot;acc:p51959]	195	17738.5	13995.6	1.26743
cyclin g2. [swissprot;acc:q16589]	194	17738.6	13995.7
cyclin h (mo15-associated protein) (p37) (p34). [swissprot;acc:p51946]	2983	0.00001	0.00001	1
cyclin k. [swissprot;acc:o75909]	3160
cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348]	1222	5735.74	6226.23	1.08551
cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]	1221	5736.34	6226.88
cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]	1220	5735.65	6226.13
cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184]	1218	5736	6226.52	1.08552
cyclin t1 (cyclin t) (cyct1). [swissprot;acc:o60563]	3002	0.00001	0.00001	1
cyclin t2. [swissprot;acc:o60583]	3171
cyclin-dependent kinase (cdc2-like) 11; death-preventing kinase. [refseq;acc:nm_015076]	2892
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	53	779.167	1390.33	1.78438
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	301	13768.2	11466	1.20078
cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552]	615	11222.2	9948.93	1.12798
cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	1793	5839.72	6227.33	1.06637
cyr61 protein precursor (cysteine-rich, angiogenic inducer, 61) (insulin-like growth factor-binding protein 10) (gig1 protein). [swissprot;acc:o00622]	2938	0.00001	0.00001	1
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	560	5480.24	6222.04	1.13536
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929]	89	2414.22	1698.12	1.4217
cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	123	24260.3	18172.1	1.33503
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	126	24250	18164.9	1.33499
cysteine-rich motor neuron 1; cysteine-rich repeat-containing protein s52 precursor. [refseq;acc:nm_016441]	1303	6334.15	6852.61	1.08185
cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]	2376	3976.48	3816.38	1.04195
cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	1024	5706.5	6245.55	1.09446
cysteine-rich secretory protein-1 precursor (crisp-1) (acidic epididymal glycoprotein homolog) (aeg-like protein) (arp). [swissprot;acc:p54107]	3018	0.00001	0.00001	1
cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108]	3150
cytidine deaminase (ec 3.5.4.5) (cytidine aminohydrolase). [swissprot;acc:p32320]	1547	5397.21	5790.45	1.07286
cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	744	12515.4	11221.1	1.11535
cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]	916	6289.72	6911.96	1.09893
cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	915
cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [swissprot;acc:q9y6n1]	928	5638.46	6194.04	1.09853
cytochrome c oxidase polypeptide va, mitochondrial precursor (ec 1.9.3.1). [swissprot;acc:p20674]	2791	0.00001	0.00001	1
cytochrome c oxidase polypeptide vib (ec 1.9.3.1) (aed). [swissprot;acc:p14854]	3009
cytochrome c oxidase subunit iv isoform 1, mitochondrial precursor (ec 1.9.3.1) (cox iv-1) (cytochrome c oxidase polypeptide iv). [swissprot;acc:p13073]	963	11773	10733.2	1.09688
cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9]	964
cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]	644	4810.85	5414.22	1.12542
cytochrome c. [swissprot;acc:p00001]	2201	5076.73	5326.29	1.04916

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.