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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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

Results: HTML CSV LaTeX

Showing element 1730 to 1779 of 8289 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Filtered  : 1

Rank	description	Hugo	Interaction Map	red	green	network_comparison
865	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	BTF3	High confidence	211.961	203.814	1.03997
866	mosaic protein lgn. [swissprot;acc:p81274]	GPSM2	Low confidence	207.56	202.355	1.02572
	signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9]	SRP68	High confidence	221.306	212.806	1.03994
867	40s ribosomal protein s3a. [swissprot;acc:p49241]	no value		225.689	234.674	1.03981
	eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371]	EIF3D	Low confidence	205.551	200.398	1.02571
868	cytochrome c oxidase subunit iv isoform 2, mitochondrial precursor (ec 1.9.3.1) (cox iv-2). [swissprot;acc:q96kj9]	COX4I2		204.037	198.928	1.02568
	diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602]	MVD	High confidence	233.298	242.571	1.03975
869	exocyst complex component sec8. [swissprot;acc:q96a65]	EXOC4		217.762	209.449	1.03969
	pap-1 binding protein. [refseq;acc:nm_031288]	ZNHIT4	Low confidence	213.16	218.629	1.02566
870	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	HNRPM		208.623	213.975	1.02565
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	no value	High confidence	211.908	203.832	1.03962
871	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	CPSF2		110.2	114.552	1.03949
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	HPRT1	Low confidence	191.561	186.777	1.02561
872	heterogeneous nuclear ribonucleoprotein k (hnrnp k) (dc-stretch binding protein) (csbp) (transformation upregulated nuclear protein) (tunp). [swissprot;acc:q07244]	HNRPK	High confidence	224.413	233.272	1.03948
	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	NDUFA5	Low confidence	203.141	198.068	1.02561
873	nadh-ubiquinone oxidoreductase 30 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-30kd) (ci-30kd). [swissprot;acc:o75489]	PTPMT1
	u4/u6 small nuclear ribonucleoprotein prp4 (u4/u6 snrnp 60 kda protein) (wd splicing factor prp4) (hprp4). [swissprot;acc:o43172]	PRPF4	High confidence	224.413	233.272	1.03948
874	5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619]	PRKAG1		212.002	203.954	1.03946
	eukaryotic translation initiation factor 3 subunit 6 (eif-3 p48) (eif3e) (mammary tumor-associated protein int-6) (viral integration site protein int-6). [swissprot;acc:q64252]	EIF3E	Low confidence	203.141	198.068	1.02561
875	5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646]	PRKAA2	High confidence	212.002	203.954	1.03946
	transcription factor-like nuclear regulator; putative transcription regulation nuclear protein; putative transcription factor-like nuclear regulator; tata box binding protein (tbp)-associated factor, rna polymerase iii, gtf3b subunit 1; b''90 component. [refseq;acc:nm_018429]	BDP1	Low confidence	203.139	198.068	1.0256
876	5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131]	PRKAA1	High confidence	212.002	203.954	1.03946
	gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [swissprot;acc:o75936]	BBOX1	Low confidence	203.744	198.658	1.0256
877	5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741]	PRKAB2	High confidence	212.002	203.954	1.03946
	probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]	DHX35	Low confidence	205.571	200.44	1.0256
878	5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9]	PRKAG3	High confidence	212.002	203.954	1.03946
	potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]	ATP11A	Low confidence	203.744	198.658	1.0256
879	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	no value		203.354	198.284	1.02557
	5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478]	PRKAB1	High confidence	212.002	203.954	1.03946
880	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	PRKAG2
	ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350]	RRM2	Low confidence	201.49	196.469	1.02556
881	l-myc-1 proto-oncogene protein. [swissprot;acc:p12524]	MYCL1	High confidence	227.604	219.001	1.03928
	max protein. [swissprot;acc:p25912]	MAX	Low confidence	204.973	199.865	1.02556
882	n-myc proto-oncogene protein. [swissprot;acc:p04198]	MYCN	High confidence	227.601	219.008	1.03924
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	STX1A	Low confidence	210.979	205.723	1.02555
883	ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546]	GABPA	High confidence	227.596	219.017	1.03917
	nadh-ubiquinone oxidoreductase mlrq subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-mlrq) (ci-mlrq). [swissprot;acc:o00483]	no value	Low confidence	202.572	197.533	1.02551
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]		High confidence	227.596	219.017	1.03917
	nadh:ubiquinone oxidoreductase mlrq subunit homolog (nuoms). [swissprot;acc:q9nrx3]	NDUFA4L2	Low confidence	202.572	197.533	1.02551
885	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]	CDC5L
	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]	NDUFS8	High confidence	227.596	219.017	1.03917
886	dna ligase iv (ec 6.5.1.1) (polydeoxyribonucleotide synthase [atp]). [swissprot;acc:p49917]	LIG4	Low confidence	202.568	197.535	1.02548
	elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60]	ELOVL1	High confidence	227.596	219.018	1.03917
887	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	EIF4E	Low confidence	202.277	197.255	1.02546
	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	TBL3	High confidence	244.155	234.96	1.03913
888	eukaryotic translation initiation factor 4e binding protein 2; eukaryotic translation initiation factor-4e binding protein-1. [refseq;acc:nm_004096]	EIF4EBP2	Low confidence	202.277	197.255	1.02546
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	no value	High confidence	212.027	204.05	1.03909
889	alpha-nac protein. [sptrembl;acc:q9h009]			212.028	204.053	1.03908
	eukaryotic translation initiation factor 4e binding protein 3; eukaryotic initiation factor 4e-binding protein 3. [refseq;acc:nm_003732]	ANKHD1-EIF4EBP3	Low confidence	202.277	197.255	1.02546
890	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	BAIAP3

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.