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	red	green	network_comparison

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

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.