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

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank	Gene	Hugo	Value Type	description	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	Value Type	description	Network Comparison Type	red	green	network_comparison
382	PARK2	Measured	parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562]	Divided	4533.74	5279.4	1.16447
	RPS23	Rooted	40s ribosomal protein s23. [swissprot;acc:p39028]		49.8325	45.2077	1.1023
	SON	Measured	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]	Subtracted	2397.19	3343.62	946.43
	TAF7L	Ranked	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]	Divided	200.791	183.66	1.09328
	TBC1D5	Squared	tbc1 domain family member 5. [swissprot;acc:q92609]	Subtracted	30286.5	36362	6075.5
	TIPRL	Rooted	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]		66.4284	60.0004	6.428
383	no value	Measured	hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631]	Divided	4533.74	5279.4	1.16447
		Squared	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]		15043.7	18560.1	1.23375
		Rooted	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	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	Ranked	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]		237.862	217.739	1.09242
	SRP9	Measured	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	Subtracted	4247.36	5192.61	945.25
	TRUB1	Ranked	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]		236.245	255.113	18.868
	TULP1	Squared	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]		30286.5	36362	6075.5
384	no value	Measured	cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	Divided	4533.74	5279.4	1.16447
		Ranked	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Subtracted	227.575	208.756	18.819
		Rooted	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	Divided	50.7723	46.0607	1.10229
			u6 snrna-associated sm-like protein lsm2 (small nuclear ribonuclear protein d homolog) (g7b) (snrnp core sm-like protein sm-x5). [swissprot;acc:q9y333]	Subtracted	56.185	62.6036	6.4186
	E2F1	Ranked	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]	Divided	266.421	244.236	1.09083
	HARS2	Measured	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	Subtracted	8061.05	9002.33	941.28
	SYNCRIP	Squared	ns1-associated protein 1. [refseq;acc:nm_006372]	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	Rooted	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]		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	Ranked	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]		266.421	244.236	1.09083
	HARS	Measured	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	Subtracted	8056.09	8996.46	940.37
	HNRNPR	Squared	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Divided	15043.7	18560.1	1.23375
	NUMBL		numb-like protein (numb-r). [swissprot;acc:q9y6r0]	Subtracted	30286.5	36362	6075.5
	PSIP1	Measured	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	Divided	4533.74	5279.4	1.16447
	SNRPF	Ranked	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Subtracted	227.575	208.756	18.819
386	no value	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262]		1833.01	892.67	940.34
		Squared	scratch; scratch 1. [refseq;acc:nm_031309]	Divided	40388.9	49827.5	1.23369
	CLEC3B	Rooted	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	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	Measured	60s ribosomal protein l8. [swissprot;acc:p25120]		4533.74	5279.4	1.16447
	RPS14	Ranked	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]		242.238	264.11	1.09029
	RPS9		40s ribosomal protein s9. [swissprot;acc:p46781]	Subtracted	238.986	257.784	18.798
	TULP3	Squared	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]		30286.5	36362	6075.5
387	no value	Ranked	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Divided	242.238	264.11	1.09029
		Rooted	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		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	Ranked	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]		56.6768	75.3531	18.6763
	EIF4G1	Squared	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Divided	15053	18568	1.23351
	GNG12	Measured	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6]	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	Squared	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]	Subtracted	30286.5	36362	6075.5
388	no value	Ranked	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Divided	227.575	208.756	1.09015
		Squared	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]		40315.7	49716.4	1.23318
	ARID1A	Measured	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	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.