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

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Showing element 475 to 515 of 515 in total

Network Comparison Type  : Subtracted
Interaction Map  : High confidence
Value Type  : Ranked
Filtered  : 1
red  : 0
green  : 0
network_comparison  : 0

description	Rank	Hugo
tubulin-specific chaperone a (tubulin-folding cofactor a) (cfa) (tcp1-chaperonin cofactor a). [swissprot;acc:o75347]	2817	TBCA
tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925]	2858	RYK
ubiquitin carboxyl-terminal hydrolase 13 (ec 3.1.2.15) (ubiquitin thiolesterase 13) (ubiquitin-specific processing protease 13) (deubiquitinating enzyme 13) (isopeptidase t-3) (isot-3). [swissprot;acc:q92995]	3192	USP13
ubiquitin carboxyl-terminal hydrolase 5 (ec 3.1.2.15) (ubiquitin thiolesterase 5) (ubiquitin-specific processing protease 5) (deubiquitinating enzyme 5) (isopeptidase t). [swissprot;acc:p45974]	3075	USP5
ubiquitin protein ligase. [refseq;acc:nm_130466]	2902	UBE3B
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]	2828	no value
ubiquitin-conjugating enzyme e2-24 kda (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2-epf5). [swissprot;acc:q16763]	3094	UBE2S
ubiquitin-like protein nedd8. [swissprot;acc:q15843]	3001	NEDD8
udp glycosyltransferase 2 family, polypeptide a1; udp glucuronosyltransferase 2 family, polypeptide a1. [refseq;acc:nm_006798]	2810	UGT2A1
udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224]	2835	UGT1A9
udp-glucuronosyltransferase 2b10 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:p36537]	3085	UGT2B10
udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	2819	no value
udp-glucuronosyltransferase 2b15 precursor, microsomal (ec 2.4.1.17) (udpgt) (udpgth-3) (hlug4). [swissprot;acc:p54855]	3086
udp-glucuronosyltransferase 2b17 precursor, microsomal (ec 2.4.1.17) (udpgt) (c19-steroid specific udp-glucuronosyltransferase). [swissprot;acc:o75795]	2793
udp-glucuronosyltransferase 2b28 precursor, microsomal (ec 2.4.1.17). [swissprot;acc:q9by64]	2979	UGT2B28
udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]	2889	UGT2B4
udp-glucuronosyltransferase 2b7 precursor, microsomal (ec 2.4.1.17) (udpgt) (3,4-catechol estrogen specific) (udpgth-2). [swissprot;acc:p16662]	2818	UGT2B7
uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	3030	C6orf35
uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]	2772	NUDT14
uroporphyrinogen decarboxylase (ec 4.1.1.37) (uro-d) (upd). [swissprot;acc:p06132]	3010	UROD
vaccinia related kinase 1; vaccinia-related kinase-1. [refseq;acc:nm_003384]	3136	VRK1
vaccinia related kinase 2; vaccinia-related kinase-2. [refseq;acc:nm_006296]	3204	VRK2
vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787]	2782	ATP6AP2
vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase m9.2 subunit) (v-atpase 9.2 kda membrane accessory protein). [swissprot;acc:o15342]	3055	ATP6V0E1
vacuolar protein sorting factor 4a; skd1-homolog; vacuolar sorting protein 4. [refseq;acc:nm_013245]	2993	VPS4A
vacuolar proton-atpase subunit. [sptrembl;acc:q8nhe4]	2821	ATP6V0E2
vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692]	3066	VEGFA
vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [swissprot;acc:p49765]	2811	VEGFB
vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [swissprot;acc:q93034]	2840	CUL5
vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106]	3157	SCFD1
vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0]	3123	VAPA
vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292]	3023	VAPB
vps28 protein homolog. [swissprot;acc:q9uk41]	2871	VPS28
wd-repeat containing protein ciao 1. [swissprot;acc:o76071]	2927	CIAO1
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	3218	MLXIPL
wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882]	3109	WISP1
wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880]	3065	WISP3
xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989]	2882	XDH
zinc finger daz interacting protein 1. [refseq;acc:nm_014934]	2981	DZIP1
zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5]	2822	SLC30A1
zinc transporter 3 (znt-3). [swissprot;acc:q99726]	3049	SLC30A3

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.