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 1251 to 1300 of 3228 in total

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

description	Rank	red	green	network_comparison
hepatocyte nuclear factor 4-alpha (hnf-4-alpha) (transcription factor hnf-4) (transcription factor 14). [swissprot;acc:p41235]	1115	251.863	258.829	1.02766
hepatocyte nuclear factor 4-gamma (hnf-4-gamma). [swissprot;acc:q14541]	1112
hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	835	231.734	222.222	1.0428
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	831
heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [swissprot;acc:p09651]	2129	221.248	222.788	1.00696
heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [swissprot;acc:p51991]	2121
heterogeneous nuclear ribonucleoprotein f (hnrnp f). [swissprot;acc:p52597]	1858	217.893	215.545	1.01089
heterogeneous nuclear ribonucleoprotein h (hnrnp h). [swissprot;acc:p31943]	1859	217.895	215.547
heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795]	1860
heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [swissprot;acc:p31942]	1856	217.892	215.543	1.0109
heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	872	224.413	233.272	1.03948
heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	1041	186.774	181.099	1.03134
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	367	234.146	256.627	1.09601
heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	250	237.302	212.41	1.11719
heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [swissprot;acc:p22626]	2134	221.248	222.788	1.00696
heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	482	237.109	254.667	1.07405
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6]	2021	208.601	210.464	1.00893
high mobility group protein 1 (hmg-1). [swissprot;acc:p09429]	2989	0.00001	0.00001	1
high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]	3144
high mobility group protein 2 (hmg-2). [swissprot;acc:p26583]	2856
high mobility group protein 4 (hmg-4) (high mobility group protein 2a) (hmg-2a). [swissprot;acc:o15347]	3203
high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	2787
high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083]	2876
high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	2863
high-mobility group 20a. [refseq;acc:nm_018200]	125	208.588	171.778	1.21429
high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339]	124	208.52	171.595	1.21519
highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101]	440	231.802	249.983	1.07843
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	788	138.705	132.538	1.04653
histidine ammonia-lyase (ec 4.3.1.3) (histidase). [swissprot;acc:p42357]	2169	215.925	214.481	1.00673
histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	1715	206.549	203.844	1.01327
histidine-rich membrane protein ke4. [swissprot;acc:q92504]	2718	216.52	216.632	1.00052
histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	1920	187.292	185.413	1.01013
histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	1919	187.231	185.349	1.01015
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929]	182	277.546	240.461	1.15422
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	279	252.644	228.42	1.10605
histone deacetylase 1 (hd1). [swissprot;acc:q13547]	777	225.989	215.53	1.04853
histone deacetylase 11 (hd11). [swissprot;acc:q96db2]	2376	212.724	213.574	1.004
histone deacetylase 2 (hd2). [swissprot;acc:q92769]	775	226.003	215.541	1.04854
histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]	2813	0.00001	0.00001	1
histone deacetylase 4 (hd4). [swissprot;acc:p56524]	2424	220.682	221.472	1.00358
histone deacetylase 5 (hd5) (antigen ny-co-9). [swissprot;acc:q9uql6]	2423		221.471
histone deacetylase 6 (hd6). [swissprot;acc:q9ubn7]	3152	0.00001	0.00001	1
histone deacetylase 9 (hd9) (hd7b) (hd7). [swissprot;acc:q9ukv0]	2425	220.682	221.472	1.00358
histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]	2784	0.00001	0.00001	1
histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]	2767
histone h2a.e (h2a/e). [swissprot;acc:q99878]	2765
histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]	2769
histone h2a.x (h2a/x). [swissprot;acc:p16104]	2768
histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]	2852
histone h2b. [refseq;acc:nm_175055]	608	247.47	233.441	1.0601

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.