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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 2858 to 2907 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
715	dendritic cell protein. [refseq;acc:nm_006360]	Measured	6593.17	7364.55	1.117
	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]	Rooted	61.0097	65.3071	1.07044
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	Squared	25911.5	30281.9	1.16867
716	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
	cpz gene product. [refseq;acc:nm_003652]	Ranked	223.121	211.685	1.05402
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Rooted	61.0098	65.3071	1.07044
	potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	Measured	6593.17	7364.55	1.117
717	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Ranked	223.121	211.685	1.05402
	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]	Measured	6593.17	7364.55	1.117
	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Rooted	61.0111	65.3081	1.07043
	sec13-related protein. [swissprot;acc:p55735]	Squared	25911.7	30282.1	1.16867
718	cpz gene product. [refseq;acc:nm_003652]	Measured	6593.17	7364.55	1.117
	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	Rooted	60.7498	65.0218	1.07032
	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	Ranked	223.121	211.685	1.05402
	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]	Squared	25911.5	30281.9	1.16867
719	carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]	Measured	6593.17	7364.55	1.117
	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	Ranked	247.769	235.074	1.054
	phenylalanine-trna synthetase. [refseq;acc:nm_006567]	Rooted	60.7498	65.0218	1.07032
	yeast sec31p homolog. [refseq;acc:nm_014933]	Squared	25911.7	30282.1	1.16867
720	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	Ranked	231.92	244.435	1.05396
	jm1 protein. [refseq;acc:nm_014008]	Rooted	61.5849	65.9155	1.07032
	potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	Measured	6593.17	7364.55	1.117
	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]	Squared	25911.5	30281.9	1.16867
721	exocyst complex component sec10 (hsec10). [swissprot;acc:o00471]	Ranked	214.765	203.8	1.0538
	peptidylprolyl isomerase-like 4; cyclophilin-type peptidyl-prolyl cis-trans isomerase; ppiase; serologically defined breast cancer antigen ny-br-18. [refseq;acc:nm_139126]	Rooted	60.8463	65.123	1.07029
	syntaxin 7. [swissprot;acc:o15400]	Measured	5580.97	6233.52	1.11692
	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]	Squared	25911.7	30282.1	1.16867
722	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	Rooted	58.4551	62.5601	1.07022
	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]	Squared	25911.7	30282.1	1.16867
	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	Measured	8061.05	9002.33	1.11677
	trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280]	Ranked	217.952	206.902	1.05341
723	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]	Squared	25911.5	30281.9	1.16867
	dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388]	Rooted	51.7007	48.3103	1.07018
	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	Measured	8056.09	8996.46	1.11673
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	Ranked	244.842	232.577	1.05274
724	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]
	ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]	Squared	25911.7	30282.1	1.16867
	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	Measured	5384.41	6012.82	1.11671
	syntaxin 12. [refseq;acc:nm_177424]	Rooted	61.3557	65.66	1.07015
725	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]		57.5045	53.7387	1.07008
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Ranked	235.296	247.673	1.0526
	phenylalanine-trna synthetase. [refseq;acc:nm_006567]	Measured	5384.41	6012.82	1.11671
	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]	Squared	25911.7	30282.1	1.16867
726	dna mismatch repair protein mlh3 (mutl protein homolog 3). [swissprot;acc:q9uhc1]	Measured	6327.86	7064.13	1.11635
	ftsj homolog 3; likely ortholog of mouse ectoplacental cone, invasive trophoblast giant cells, extraembryonic ectoderm and chorion sequence 3. [refseq;acc:nm_017647]	Ranked	244.495	232.419	1.05196
	secretory pathway component sec31b-1. [refseq;acc:nm_015490]	Squared	25911.7	30282.1	1.16867
	transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453]	Rooted	51.4482	55.0529	1.07006
727	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	Measured	7087.23	7911.25	1.11627
	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	Ranked	208.873	219.71	1.05188
	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Rooted	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
- 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.