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

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Showing element 851 to 900 of 3228 in total

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

Rank	description	red	network_comparison	green
851	trs85 homolog. [swissprot;acc:q9y2l5]	107.842	1.04161	112.329
852	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	193.114	1.04154	185.412
853	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	108.289	1.0414	112.772
854	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
855	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	178.514	1.04138	171.42
856	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	215.028	1.04068	206.623
857	putatative 28 kda protein. [refseq;acc:nm_020143]	227.241	1.0406	236.467
858	syntaxin 12. [refseq;acc:nm_177424]	217.446	1.04043	208.997
859	60s ribosomal protein l39. [swissprot;acc:p02404]	234.025	1.04031	224.958
860	60s ribosomal protein l18a. [swissprot;acc:q02543]
861	40s ribosomal protein s19. [swissprot;acc:p39019]
862	60s ribosomal protein l31. [swissprot;acc:p12947]
863	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	240.194	1.03999	230.957
864	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
865	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	211.961	1.03997	203.814
866	signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	221.306	1.03994	212.806
867	40s ribosomal protein s3a. [swissprot;acc:p49241]	225.689	1.03981	234.674
868	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	233.298	1.03975	242.571
869	exocyst complex component sec8. [swissprot;acc:q96a65]	217.762	1.03969	209.449
870	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	211.908	1.03962	203.832
871	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	110.2	1.03949	114.552
872	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	224.413	1.03948	233.272
873	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]
874	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	212.002	1.03946	203.954
875	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]
876	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]
877	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]
878	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]
879	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]
880	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
881	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	227.604	1.03928	219.001
882	n-myc proto-oncogene protein. [swissprot;acc:p04198]	227.601	1.03924	219.008
883	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	227.596	1.03917	219.017
884	ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]
885	nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217]
886	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]			219.018
887	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	244.155	1.03913	234.96
888	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	212.027	1.03909	204.05
889	alpha-nac protein. [sptrembl;acc:q9h009]	212.028	1.03908	204.053
890	syntaxin 7. [swissprot;acc:o15400]	217.181		209.012
891	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	212.028	1.03907	204.055
892	di-ras2. [refseq;acc:nm_017594]
893	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	227.585	1.03903	219.037
894	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	217.491	1.03902	209.323
895	phenylalanine-trna synthetase. [refseq;acc:nm_006567]
896	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	230.811	1.03888	239.785
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	272.878	1.03882	283.472
898	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	229.171	1.03874	238.048
899	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]
900	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]

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.