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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 6336 to 6385 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
3168	cop-coated vesicle membrane protein p24 precursor (p24a). [swissprot;acc:q15363]	Subtracted	0	0	0
3169	transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [swissprot;acc:q12986]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3170	ecotropic virus integration 1 site protein. [swissprot;acc:q03112]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3171	cyclin t2. [swissprot;acc:o60583]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3172	hormone sensitive lipase (ec 3.1.1.-) (hsl). [swissprot;acc:q05469]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3173	phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [refseq;acc:nm_002647]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3174	transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [swissprot;acc:q9hd45]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3175	tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [swissprot;acc:p05214]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3176	phosphate carrier protein, mitochondrial precursor (ptp). [swissprot;acc:q00325]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3177	ergic-53 protein precursor (er-golgi intermediate compartment 53 kda protein) (lectin, mannose-binding 1) (gp58) (intracellular mannose specific lectin mr60). [swissprot;acc:p49257]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3178	transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3179	carcinoma related gene. [refseq;acc:nm_016041]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3180	3-hydroxyacyl-coa dehydrogenase type ii (ec 1.1.1.35) (type ii hadh) (endoplasmic reticulum-associated amyloid beta-peptide binding protein) (short-chain type dehydrogenase/reductase xh98g2). [swissprot;acc:q99714]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3181	fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [swissprot;acc:p51648]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3182	transcription factor e2-alpha (immunoglobulin enhancer binding factor e12/e47) (transcription factor-3) (tcf-3) (immunoglobulin transcription factor-1) (transcription factor itf-1) (kappa-e2-binding factor). [swissprot;acc:p15923]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3183	core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [swissprot;acc:q13951]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3184	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [swissprot;acc:p23497]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3185	ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [swissprot;acc:p22830]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3186	protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3187	doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [refseq;acc:nm_021240]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3188	connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [swissprot;acc:o76076]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3189	ring finger protein 4. [swissprot;acc:p78317]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3190	myotubularin-related protein 1 (ec 3.1.3.-). [swissprot;acc:q13613]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3191	amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [refseq;acc:nm_006380]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3192	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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
3193	rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [swissprot;acc:p50395]	Divided	0.00001	0.00001	1

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.