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

Results: HTML CSV LaTeX

Showing element 3051 to 3100 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	Value Type	Network Comparison Type	red	green	network_comparison
382	PARK2	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	Measured	Divided	4533.74	5279.4	1.16447
	RPS23	40s ribosomal protein s23. [swissprot;acc:p39028]	Rooted		49.8325	45.2077	1.1023
	SON	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583]	Measured	Subtracted	2397.19	3343.62	946.43
	TAF7L	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885]	Ranked	Divided	200.791	183.66	1.09328
	TBC1D5	tbc1 domain family member 5. [swissprot;acc:q92609]	Squared	Subtracted	30286.5	36362	6075.5
	TIPRL	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Rooted		66.4284	60.0004	6.428
383	no value	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	Squared	Divided	15043.7	18560.1	1.23375
		hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	Measured		4533.74	5279.4	1.16447
		hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	Rooted	Subtracted	46.1476	52.5742	6.4266
	MRPS12	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]		Divided	49.8325	45.2077	1.1023
	RBM39	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	Ranked		237.862	217.739	1.09242
	SRP9	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Measured	Subtracted	4247.36	5192.61	945.25
	TRUB1	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Ranked		236.245	255.113	18.868
	TULP1	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	Squared		30286.5	36362	6075.5
384	no value	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Rooted	Divided	50.7723	46.0607	1.10229
		cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	Measured		4533.74	5279.4	1.16447
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Ranked	Subtracted	227.575	208.756	18.819
		u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Rooted		56.185	62.6036	6.4186
	E2F1	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Ranked	Divided	266.421	244.236	1.09083
	HARS2	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	Measured	Subtracted	8061.05	9002.33	941.28
	SYNCRIP	ns1-associated protein 1. [refseq;acc:nm_006372]	Squared	Divided	15043.7	18560.1	1.23375
	VPS29	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]		Subtracted	30286.5	36362	6075.5
385	ATG12	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	Rooted		87.4586	81.0798	6.3788
	BCCIP	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]		Divided	50.7723	46.0607	1.10229
	E2F2	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Ranked		266.421	244.236	1.09083
	HARS	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	Measured	Subtracted	8056.09	8996.46	940.37
	HNRNPR	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Squared	Divided	15043.7	18560.1	1.23375
	NUMBL	numb-like protein (numb-r). [swissprot;acc:q9y6r0]		Subtracted	30286.5	36362	6075.5
	PSIP1	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	Measured	Divided	4533.74	5279.4	1.16447
	SNRPF	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Ranked	Subtracted	227.575	208.756	18.819
386	no value	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]	Measured		1833.01	892.67	940.34
		scratch; scratch 1. [refseq;acc:nm_031309]	Squared	Divided	40388.9	49827.5	1.23369
	CLEC3B	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	Rooted	Subtracted	86.1101	92.4812	6.3711
	EIF1B	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]		Divided	50.0513	45.4124	1.10215
	RPL8	60s ribosomal protein l8. [swissprot;acc:p25120]	Measured		4533.74	5279.4	1.16447
	RPS14	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	Ranked		242.238	264.11	1.09029
	RPS9	40s ribosomal protein s9. [swissprot;acc:p46781]		Subtracted	238.986	257.784	18.798
	TULP3	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]	Squared		30286.5	36362	6075.5
387	no value	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Ranked	Divided	242.238	264.11	1.09029
		60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Rooted		50.3345	45.6718	1.10209
		cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]		Subtracted	98.2298	91.8648	6.365
	ATG4A	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	Ranked		56.6768	75.3531	18.6763
	EIF4G1	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Squared	Divided	15053	18568	1.23351
	GNG12	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	Measured	Subtracted	1833.01	892.67	940.34
	HDGF	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]		Divided	4533.74	5279.4	1.16447
	VPS35	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]	Squared	Subtracted	30286.5	36362	6075.5
388	no value	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]		Divided	40315.7	49716.4	1.23318
		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Ranked		227.575	208.756	1.09015
	ARID1A	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Measured	Subtracted	6252.58	7192.88	940.3
	HDGFL1	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]		Divided	4533.74	5279.4	1.16447

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.