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	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 3130 to 3179 of 3228 in total

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

Rank	Hugo	description
3130	PFDN4	prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4]
3131	C20orf24	protein c20orf24 (rab5-interacting protein) (rip5) (pnas-11). [swissprot;acc:q9buv8]
3132	R3HDML	r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491]
3133	IFT52	ngd5 protein homolog (cgi-53). [swissprot;acc:q9y366]
3134	RABGGTA	rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696]
3135	SEC23A	protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436]
3136	VRK1	vaccinia related kinase 1; vaccinia-related kinase-1. [refseq;acc:nm_003384]
3137	CDKL1	serine/threonine-protein kinase kkialre (ec 2.7.1.-) (cyclin-dependent kinase-like 1). [swissprot;acc:q00532]
3138	C14orf124	hcdi protein. [refseq;acc:nm_020195]
3139	BRD1	bromodomain-containing protein 1 (br140-like protein). [swissprot;acc:o95696]
3140	MYH9	myosin heavy chain, nonmuscle type a (cellular myosin heavy chain, type a) (nonmuscle myosin heavy chain-a) (nmmhc-a). [swissprot;acc:p35579]
3141	TTLL1	tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922]
3142	PACSIN2	protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0]
3143	PICK1	prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5]
3144	HMG1L10	high mobility group protein 1-like 10 (hmg-1l10). [swissprot;acc:q9ugv6]
3145	UPB1	beta-ureidopropionase (ec 3.5.1.6) (beta-alanine synthase) (n-carbamoyl-beta-alanine amidohydrolase) (bup-1). [swissprot;acc:q9ubr1]
3146	DERL3	putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]
3147	HSD3B7	3 beta-hydroxy-delta 5-c27-steroid oxidoreductase. [refseq;acc:nm_025193]
3148	no value	muts protein homolog 5. [swissprot;acc:o43196]
3149	BRPF3	bromodomain and phd finger-containing protein 3 (fragment). [swissprot;acc:q9uld4]
3150	CRISP3	cysteine-rich secretory protein-3 precursor (crisp-3) (sgp28 protein). [swissprot;acc:p54108]
3151	MSH2	dna mismatch repair protein msh2. [swissprot;acc:p43246]
3152	HDAC6	histone deacetylase 6 (hd6). [swissprot;acc:q9ubn7]
3153	LRRFIP2	leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309]
3154	NUP50	nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [swissprot;acc:q9ukx7]
3155	TGFB2	transforming growth factor beta 2 precursor (tgf-beta 2) (glioblastoma-derived t-cell suppressor factor) (g-tsf) (bsc-1 cell growth inhibitor) (polyergin) (cetermin). [swissprot;acc:p08112]
3156	TEKT2	tektin 2 (tektin-t) (testicular tektin b1-like protein). [swissprot;acc:q9uif3]
3157	SCFD1	vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106]
3158	ITGA6	integrin alpha-6 precursor (vla-6) (cd49f). [swissprot;acc:p23229]
3159	TNRC6A	trinucleotide repeat containing 6; edie; gw182 autoantigen. [refseq;acc:nm_014494]
3160	CCNK	cyclin k. [swissprot;acc:o75909]
3161	BRAP	brca1 associated protein. [refseq;acc:nm_006768]
3162	PEBP1	phosphatidylethanolamine-binding protein (pebp) (prostatic binding protein) (hcnppp) (neuropolypeptide h3) (raf kinase inhibitor protein) (rkip) [contains: hippocampal cholinergic neurostimulating peptide (hcnp)]. [swissprot;acc:p30086]
3163	CNOT3	ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516]
3164	TFAP2C	transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [swissprot;acc:q92754]
3165	PIGS	gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [swissprot;acc:q96s52]
3166	MTMR2	myotubularin-related protein 2 (ec 3.1.3.-). [swissprot;acc:q13614]
3167	ZW10	centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264]
3168	TMED2	cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363]
3169	NFX1	transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [swissprot;acc:q12986]
3170	EVI1	ecotropic virus integration 1 site protein. [swissprot;acc:q03112]
3171	CCNT2	cyclin t2. [swissprot;acc:o60583]
3172	LIPE	hormone sensitive lipase (ec 3.1.1.-) (hsl). [swissprot;acc:q05469]
3173	PIK3C3	phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [refseq;acc:nm_002647]
3174	TM9SF3	transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45]
3175	TUBA3D	tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [swissprot;acc:p05214]
3176	SLC25A3	phosphate carrier protein, mitochondrial precursor (ptp). [swissprot;acc:q00325]
3177	LMAN1	ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [swissprot;acc:p49257]
3178	no value	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]
3179	DERL2	carcinoma related gene. [refseq;acc:nm_016041]

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.