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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

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Showing element 850 to 899 of 3228 in total

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

Rank	Hugo	description	red	green	network_comparison
850	CPSF4	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	107.842	112.329	1.04161
851	KIAA1012	trs85 homolog. [swissprot;acc:q9y2l5]
852	HPRT1	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	193.114	185.412	1.04154
853	WDR33	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	108.289	112.772	1.0414
854	CPSF1	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
855	CLEC3B	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	178.514	171.42	1.04138
856	XPR1	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	215.028	206.623	1.04068
857	PNO1	putatative 28 kda protein. [refseq;acc:nm_020143]	227.241	236.467	1.0406
858	STX12	syntaxin 12. [refseq;acc:nm_177424]	217.446	208.997	1.04043
859	no value	60s ribosomal protein l39. [swissprot;acc:p02404]	234.025	224.958	1.04031
860		60s ribosomal protein l18a. [swissprot;acc:q02543]
861	RPS19	40s ribosomal protein s19. [swissprot;acc:p39019]
862	RPL31	60s ribosomal protein l31. [swissprot;acc:p12947]
863	CSNK2A1P	casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138]	240.194	230.957	1.03999
864	CSNK2A2	casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
865	BTF3	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	211.961	203.814	1.03997
866	SRP68	signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	221.306	212.806	1.03994
867	no value	40s ribosomal protein s3a. [swissprot;acc:p49241]	225.689	234.674	1.03981
868	MVD	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	233.298	242.571	1.03975
869	EXOC4	exocyst complex component sec8. [swissprot;acc:q96a65]	217.762	209.449	1.03969
870	no value	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	211.908	203.832	1.03962
871	CPSF2	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	110.2	114.552	1.03949
872	HNRPK	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	224.413	233.272	1.03948
873	PRPF4	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]
874	PRKAG1	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	212.002	203.954	1.03946
875	PRKAA2	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]
876	PRKAA1	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]
877	PRKAB2	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]
878	PRKAG3	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]
879	PRKAB1	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]
880	PRKAG2	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]
881	MYCL1	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	227.604	219.001	1.03928
882	MYCN	n-myc proto-oncogene protein. [swissprot;acc:p04198]	227.601	219.008	1.03924
883	GABPA	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	227.596	219.017	1.03917
884	no value	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	NDUFS8	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	ELOVL1	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]		219.018
887	TBL3	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	244.155	234.96	1.03913
888	no value	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	212.027	204.05	1.03909
889		alpha-nac protein. [sptrembl;acc:q9h009]	212.028	204.053	1.03908
890	STX7	syntaxin 7. [swissprot;acc:o15400]	217.181	209.012
891	DIRAS1	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	212.028	204.055	1.03907
892	DIRAS2	di-ras2. [refseq;acc:nm_017594]
893	MYC	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	227.585	219.037	1.03903
894	FARSA	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	217.491	209.323	1.03902
895	FARS2	phenylalanine-trna synthetase. [refseq;acc:nm_006567]
896	POLR2J	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	230.811	239.785	1.03888
897	PDPK1	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	272.878	283.472	1.03882
898	no value	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	229.171	238.048	1.03874
899	TXNDC2	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]

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
- Hugo is the HGNC identifier if it exists
- 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.