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

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Showing element 1318 to 1367 of 3228 in total

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

description	Rank	green	network_comparison	red
homeobox protein barh-like 1. [swissprot;acc:q9hbu1]	582	252.492	1.06411	237.28
homeobox protein barh-like 2. [swissprot;acc:q9umq3]	587
homeobox protein cux-2 (cut-like 2) (fragment). [swissprot;acc:o14529]	557	194.371	1.06637	207.272
homeobox protein dlx-2. [swissprot;acc:q07687]	2337	230.294	1.00452	229.258
homeobox protein dlx-3. [swissprot;acc:o60479]	2340
homeobox protein dlx-5. [swissprot;acc:p56178]	2338
homeobox protein engrailed-2 (hu-en-2). [swissprot;acc:p19622]	1167	213.784	1.02626	219.399
homeobox protein hlx1 (homeobox protein hb24). [swissprot;acc:q14774]	7	322	1.49767	215
homeobox protein hox-a10 (hox-1h) (hox-1.8) (pl). [swissprot;acc:p31260]	614	202.125	1.06002	214.257
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	686	125.389	1.05602	132.413
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	685
homeobox protein hox-a9 (hox-1g). [swissprot;acc:p31269]	616	202.132	1.05999	214.257
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	680	125.389	1.05602	132.413
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	684
homeobox protein hox-b9 (hox-2e) (hox-2.5). [swissprot;acc:p17482]	615	202.132	1.05999	214.257
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	679	125.389	1.05602	132.413
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	681
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	682
homeobox protein hox-c9 (hox-3b). [swissprot;acc:p31274]	617	202.135	1.05997	214.257
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	683	125.389	1.05602	132.413
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	632	202.166	1.05979	214.254
homeobox protein meis1. [swissprot;acc:o00470]	1783	203.874	1.01206	206.332
homeobox protein meis2 (meis1-related protein 1). [swissprot;acc:o14770]	1784
homeobox protein meis3 (meis1-related protein 2) (fragment). [swissprot;acc:q99687]	1788
homeobox protein nkx-6.1. [swissprot;acc:p78426]	2859	0.00001	1	0.00001
homeobox protein otx1. [swissprot;acc:p32242]	1520	240.098	1.01778	244.367
homeobox protein otx2. [swissprot;acc:p32243]	1521	240.212	1.01776	244.478
homeobox protein prh (hematopoietically expressed homeobox) (homeobox protein hex). [swissprot;acc:q03014]	1709	195.385	1.01346	198.014
homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475]	1128	215.399	1.02733	221.286
homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8]	1129	215.401	1.02732	221.285
homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	107	201.998	1.24907	252.309
homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	104	202.016	1.24926	252.371
homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	108	201.995	1.24902	252.296
homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011]	3196	0.00001	1	0.00001
homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [swissprot;acc:q93099]	3053
homolog of yeast maf1. [refseq;acc:nm_032272]	1977	207.529	1.00969	209.539
hormone sensitive lipase (ec 3.1.1.-) (hsl). [swissprot;acc:q05469]	3172	0.00001	1	0.00001
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	289	246.892	1.10486	272.781
hrd1 protein isoform a; synoviolin1. [refseq;acc:nm_032431]	2231	223.246	1.00633	221.842
hsgcn1 (fragment). [sptrembl;acc:q99736]	2712	220.395	1.00057	220.521
hskin17 protein. [refseq;acc:nm_012311]	1697	214.69	1.01367	217.624
hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	2258	225.191	1.00582	223.888
human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	1486	203.989	1.01906	207.877
human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	1488
huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	1995	190.73	1.00936	188.961
huntingtin interacting protein 1 related (hip1-related) (hip 12). [swissprot;acc:o75146]	1993	190.835	1.00943	189.052
huntingtin interacting protein c. [refseq;acc:nm_012272]	195	200.417	1.13748	227.971
huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	729	219.708	1.05187	208.874
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]	949	209.826	1.0354	217.253
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	179	194.79	1.16476	226.884

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.