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

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Showing element 51 to 100 of 29840 in total

Filtered  : 0
Value Type  : Measured
Interaction Map  : High confidence
Network Comparison Type  : Divided

network_comparison	Rank	green	description	red
1.01163	463	1248.14	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	1262.65
1.01202	462	11305	leucine rich repeat (in flii) interacting protein 1. [refseq;acc:nm_004735]	11170.7
1.01229	461	1892.44	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	1915.69
1.01259	460	3739.55	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	3693.07
1.01266	459	3821.87	intersectin 1 (sh3 domain-containing protein 1a) (sh3p17). [swissprot;acc:q15811]	3774.08
1.01327	458	2668.56	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	2633.61
1.01341	457	1541.69	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]	1562.36
1.01343	456	17126	cop9 signalosome complex subunit 1 (g protein pathway suppressor 1) (gps1 protein) (mfh protein). [swissprot;acc:q13098]	17356
1.01362	455	2371.24	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	2403.53
1.01402	454	3174.79	transducin-like enhancer protein 1 (esg1). [swissprot;acc:q04724]	3219.3
1.01438	453	1356.52	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132]	1337.29
1.01496	452	1504.85	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	1527.36
1.01545	451	2642.79	26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832]	2683.61
1.01569	450	4094.09	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	4158.33
1.01634	449	5607.7	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	5699.32
1.01682	448	533.236	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	524.415
1.01735	447	2879.55	40s ribosomal protein s3a. [swissprot;acc:p49241]	2929.51
1.01787	446	1522.06	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	1549.26
1.01835	445	9808.48	mstp028 protein. [refseq;acc:nm_031954]	9988.45
1.02223	443	2379.52	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	2432.41
	444	2378.99	40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677]	2431.87
1.02335	442	6856.28	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	6699.82
1.02355	441	6303	aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468]	6158
1.02491	440	7000.85	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	6830.67
1.02503	439	546	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	532.667
1.0252	438	2853.65	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	2925.57
1.02531	437	2390	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	2331
1.0265	436	151.122	alpha-nac protein. [sptrembl;acc:q9h009]	147.221
1.02677	435	5737.71	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	5891.28
1.02736	432	103.25	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]	100.5
	433		sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
	434	206.5	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	201
1.02787	431	150.709	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	146.622
1.02803	430	10535	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	10247.8
1.02858	429	485.852	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975]	472.351
1.02953	428	14688.8	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	14267.5
1.02978	427	1161.29	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	1195.87
1.03004	426	2133.83	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	2071.59
1.03079	425	2134.56		2070.81
1.03136	424	4091.59	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	3967.18
1.03165	423	13809	fibrillin 3. [refseq;acc:nm_032447]	14246
1.03203	422	1117.36	kappa b-ras 1. [refseq;acc:nm_020345]	1153.15
1.03207	421	476.639	importin 4. [refseq;acc:nm_024658]	491.926
1.03214	420	19496	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	18889
1.03225	419	2604.71	60s ribosomal protein l18a. [swissprot;acc:q02543]	2688.7
1.03226	418	699.577	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	722.144
1.0323	417	699.324	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	721.913
1.03231	416	699.297	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	721.888
1.03232	415	699.215	zinc finger protein 232. [swissprot;acc:q9uny5]	721.814
1.03363	414	7276.12	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	7520.78

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.