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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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

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Showing element 2830 to 2879 of 3228 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
red  : 0.00001
green  : 0.00001
network_comparison  : 1

Rank	Hugo	description
2830	CSNK1G1	casein kinase i, gamma 1 isoform (ec 2.7.1.-) (cki-gamma 1). [swissprot;acc:q9hcp0]
2831	FEN1	flap endonuclease-1 (ec 3.-.-.-) (maturation factor 1) (mf1). [swissprot;acc:p39748]
2832	SEMA6B	semaphorin 6b precursor (semaphorin z) (sema z). [swissprot;acc:q9h3t3]
2833	TPM4	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]
2834	ATP5L	atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964]
2835	UGT1A9	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]
2836	COG1	conserved oligomeric golgi complex component 1. [swissprot;acc:q8wtw3]
2837	TK2	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]
2838	DCHS1	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]
2839	TAF10	transcription initiation factor tfiid 30 kda subunit (tafii-30) (tafii30). [swissprot;acc:q12962]
2840	CUL5	vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [swissprot;acc:q93034]
2841	COPS2	cop9 signalosome complex subunit 2 (signalosome subunit 2) (sgn2) (thyroid receptor interacting protein 15) (trip15). [swissprot;acc:q15647]
2842	NOLC1	nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [swissprot;acc:q14978]
2843	SENP8	sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8]
2844	FBN1	fibrillin 1 precursor. [swissprot;acc:p35555]
2845	PACSIN3	protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6]
2846	C10orf118	ctcl tumor antigen l14-2. [refseq;acc:nm_018017]
2847	DACH1	dachshund homolog isoform a. [refseq;acc:nm_080759]
2848	GTF2A1	transcription initiation factor iia alpha and beta chains (tfiia p35 and p19 subunits) (tfiia-42) (tfiial). [swissprot;acc:p52655]
2849	SNAPC3	snrna activating protein complex 50 kda subunit (snapc 50 kda subunit) (proximal sequence element-binding transcription factor beta subunit) (pse-binding factor beta subunit) (ptf beta subunit). [swissprot;acc:q92966]
2850	CDK5	cell division protein kinase 5 (ec 2.7.1.-) (tau protein kinase ii catalytic subunit) (tpkii catalytic subunit) (serine/threonine protein kinase pssalre). [swissprot;acc:q00535]
2851	ORC5L	origin recognition complex subunit 5. [swissprot;acc:o43913]
2852	HIST1H2AA	histone h2a; h2a histone family, member r. [refseq;acc:nm_170745]
2853	TIGD6	tigger transposable element derived 6. [refseq;acc:nm_030953]
2854	NARG1	transcriptional coactivator tubedown-100 isoform 1; putative n-acetyltransferase; gastric cancer antigen ga19. [refseq;acc:nm_057175]
2855	HPGD	15-hydroxyprostaglandin dehydrogenase [nad(+)] (ec 1.1.1.141) (pgdh). [swissprot;acc:p15428]
2856	HMGB2	high mobility group protein 2 (hmg-2). [swissprot;acc:p26583]
2857	PRKCD	protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [swissprot;acc:q05655]
2858	RYK	tyrosine-protein kinase ryk precursor (ec 2.7.1.112). [swissprot;acc:p34925]
2859	NKX6-1	homeobox protein nkx-6.1. [swissprot;acc:p78426]
2860	no value	importin 9. [refseq;acc:nm_018085]
2861	GNPDA2	glucosamine-6-phosphate isomerase. [refseq;acc:nm_138335]
2862	SDC3	syndecan-3 (synd3). [swissprot;acc:o75056]
2863	no value	high-glucose-regulated protein 8 (ny-ren-2 antigen). [swissprot;acc:q9y5a9]
2864	MAGOH	mago nashi protein homolog. [swissprot;acc:p50606]
2865	TAL1	t-cell acute lymphocytic leukemia-1 protein (tal-1 protein) (stem cell protein) (t-cell leukemia/lymphoma-5 protein). [swissprot;acc:p17542]
2866	STX5	syntaxin 5. [swissprot;acc:q13190]
2867	no value	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]
2868	SNORA67	eukaryotic initiation factor 4a-i (eif-4a-i) (eif4a-i). [swissprot;acc:p04765]
2869	PRPSAP1	phosphoribosyl pyrophosphate synthetase-associated protein 1 (prpp synthetase-associated protein 1) (39 kda phosphoribosypyrophosphate synthetase-associated protein) (pap39). [swissprot;acc:q14558]
2870	SH2B2	adaptor protein with pleckstrin homology and src homology 2 domains. [refseq;acc:nm_020979]
2871	VPS28	vps28 protein homolog. [swissprot;acc:q9uk41]
2872	BTBD14B	transcriptional repressor nac1. [refseq;acc:nm_052876]
2873	ITGB2	integrin beta-2 precursor (cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta-subunit) (cd18) (complement receptor c3 beta- subunit). [swissprot;acc:p05107]
2874	C21orf2	protein c21orf2 (c21orf-humf09g8.5) (yf5/a2). [swissprot;acc:o43822]
2875	CRYAA	alpha crystallin a chain. [swissprot;acc:p02489]
2876	PDE9A	high-affinity cgmp-specific 3',5'-cyclic phosphodiesterase 9a (ec 3.1.4.17). [swissprot;acc:o76083]
2877	RUNX1	runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]
2878	NDUFS2	nadh-ubiquinone oxidoreductase 49 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-49kd) (ci-49kd). [swissprot;acc:o75306]
2879	no value	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]

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.