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

Results: HTML CSV LaTeX

Showing element 2863 to 2912 of 12912 in total

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

Rank	Hugo	Value Type	description	red	green	network_comparison
716	CPXM2	Measured	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	6593.17	7364.55	1.117
	CPZ	Ranked	cpz gene product. [refseq;acc:nm_003652]	223.121	211.685	1.05402
717	CPE		carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]
	CPN1	Measured	carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169]	6593.17	7364.55	1.117
	HDAC1	Rooted	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	61.0111	65.3081	1.07043
	SEC13	Squared	sec13-related protein. [swissprot;acc:p55735]	25911.7	30282.1	1.16867
718	ATP6V1G3		vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4]	25911.5	30281.9
	CPXM1	Ranked	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	223.121	211.685	1.05402
	CPZ	Measured	cpz gene product. [refseq;acc:nm_003652]	6593.17	7364.55	1.117
	FARSA	Rooted	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	60.7498	65.0218	1.07032
719	CPE	Measured	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	6593.17	7364.55	1.117
	FARS2	Rooted	phenylalanine-trna synthetase. [refseq;acc:nm_006567]	60.7498	65.0218	1.07032
	NOL5A	Ranked	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	247.769	235.074	1.054
	SEC31A	Squared	yeast sec31p homolog. [refseq;acc:nm_014933]	25911.7	30282.1	1.16867
720	ATP6V1G1		vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348]	25911.5	30281.9
	CCDC22	Rooted	jm1 protein. [refseq;acc:nm_014008]	61.5849	65.9155	1.07032
	CPXM1	Measured	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	6593.17	7364.55	1.117
	RPLP2	Ranked	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	231.92	244.435	1.05396
721	ATP6V1E1	Squared	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543]	25911.7	30282.1	1.16867
	EXOC5	Ranked	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	214.765	203.8	1.0538
	PPIL4	Rooted	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	60.8463	65.123	1.07029
	STX7	Measured	syntaxin 7. [swissprot;acc:o15400]	5580.97	6233.52	1.11692
722	DYNC1I1	Rooted	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	58.4551	62.5601	1.07022
	GDAP1L1	Squared	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]	25911.7	30282.1	1.16867
	HARS2	Measured	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	8061.05	9002.33	1.11677
	TREH	Ranked	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	217.952	206.902	1.05341
723	no value		histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	244.842	232.577	1.05274
	DDX39	Squared	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]	25911.5	30281.9	1.16867
	HARS	Measured	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	8056.09	8996.46	1.11673
	POLR2E	Rooted	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	51.7007	48.3103	1.07018
724	no value	Ranked	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	244.842	232.577	1.05274
	FARSA	Measured	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	5384.41	6012.82	1.11671
	GDAP1	Squared	ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]	25911.7	30282.1	1.16867
	STX12	Rooted	syntaxin 12. [refseq;acc:nm_177424]	61.3557	65.66	1.07015
725	ATP6V1D	Squared	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8]	25911.7	30282.1	1.16867
	FARS2	Measured	phenylalanine-trna synthetase. [refseq;acc:nm_006567]	5384.41	6012.82	1.11671
	HNRPM	Rooted	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	57.5045	53.7387	1.07008
	MVK	Ranked	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	235.296	247.673	1.0526
726	FTSJ3		ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	244.495	232.419	1.05196
	MLH3	Measured	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	6327.86	7064.13	1.11635
	SEC31B	Squared	secretory pathway component sec31b-1. [refseq;acc:nm_015490]	25911.7	30282.1	1.16867
	TBL3	Rooted	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	51.4482	55.0529	1.07006
727	ATP6V1H	Squared	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12]	25911.5	30281.9	1.16867
	NUAK1	Ranked	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	208.873	219.71	1.05188
	RPL24	Measured	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	7087.23	7911.25	1.11627
	SF3A3	Rooted	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	59.7414	63.909	1.06976
728	ASNSD1	Measured	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	6000.23	6696.89	1.11611
	ATP6V1B2	Squared	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281]	25911.8	30282.2	1.16866
	B3GNT1	Ranked	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]	208.874	219.708	1.05187
	SF3A1	Rooted	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	59.7414	63.909	1.06976

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.