Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 3151 to 3200 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	
3151	MSH2	dna mismatch repair protein msh2. [source:swissprot;acc:p43246]	
3152	HDAC6	histone deacetylase 6 (hd6). [source:swissprot;acc:q9ubn7]	
3153	LRRFIP2	leucine rich repeat (in flii) interacting protein 2. [source:refseq;acc:nm_006309]	
3154	NUP50	nucleoporin 50 kda (nuclear pore-associated protein 60 kda-like) (pro1146). [source: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). [source:swissprot;acc:p08112]	
3156	TEKT2	tektin 2 (tektin-t) (testicular tektin b1-like protein). [source:swissprot;acc:q9uif3]	
3157	SCFD1	vesicle transport-related protein isoform a; vesicle transport-related protein. [source:refseq;acc:nm_016106]	
3158	ITGA6	integrin alpha-6 precursor (vla-6) (cd49f). [source:swissprot;acc:p23229]	
3159	TNRC6A	trinucleotide repeat containing 6; edie; gw182 autoantigen. [source:refseq;acc:nm_014494]	
3160	CCNK	cyclin k. [source:swissprot;acc:o75909]	
3161	BRAP	brca1 associated protein. [source: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)]. [source:swissprot;acc:p30086]	
3163	CNOT3	ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [source:refseq;acc:nm_014516]	
3164	TFAP2C	transcription factor ap-2 gamma (ap2-gamma) (activating enhancer- binding protein 2 gamma) (transcription factor erf-1). [source:swissprot;acc:q92754]	
3165	PIGS	gpi transamidase component pig-s (phosphatidylinositol-glycan biosynthesis, class s protein). [source:swissprot;acc:q96s52]	
3166	MTMR2	myotubularin-related protein 2 (ec 3.1.3.-). [source:swissprot;acc:q13614]	
3167	ZW10	centromere/kinetochore protein zw10 homolog. [source:swissprot;acc:o43264]	
3168	TMED2	cop-coated vesicle membrane protein p24 precursor (p24a). [source:swissprot;acc:q15363]	
3169	NFX1	transcriptional repressor nf-x1 (ec 6.3.2.-) (nuclear transcription factor, x box-binding, 1). [source:swissprot;acc:q12986]	
3170	EVI1	ecotropic virus integration 1 site protein. [source:swissprot;acc:q03112]	
3171	CCNT2	cyclin t2. [source:swissprot;acc:o60583]	
3172	LIPE	hormone sensitive lipase (ec 3.1.1.-) (hsl). [source:swissprot;acc:q05469]	
3173	PIK3C3	phosphoinositide-3-kinase, class 3; vps34; phosphatidylinositol 3-kinase, class 3. [source:refseq;acc:nm_002647]	
3174	TM9SF3	transmembrane 9 superfamily protein member 3 precursor (sm-11044 binding protein) (ep70-p-iso). [source:swissprot;acc:q9hd45]	
3175	TUBA3D	tubulin alpha-3/alpha-7 chain (alpha-tubulin 3/7). [source:swissprot;acc:p05214]	
3176	SLC25A3	phosphate carrier protein, mitochondrial precursor (ptp). [source: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). [source:swissprot;acc:p49257]	
3178		transcription initiation factor iie, beta subunit (tfiie-beta). [source:swissprot;acc:p29084]	
3179	DERL2	carcinoma related gene. [source:refseq;acc:nm_016041]	
3180	HSD17B10	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). [source:swissprot;acc:q99714]	
3181	ALDH3A2	fatty aldehyde dehydrogenase (ec 1.2.1.3) (aldehyde dehydrogenase, microsomal) (aldh class 3). [source:swissprot;acc:p51648]	
3182	TCF3	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). [source:swissprot;acc:p15923]	
3183	CBFB	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). [source:swissprot;acc:q13951]	
3184	SP100	nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [source:swissprot;acc:p23497]	
3185	FECH	ferrochelatase, mitochondrial precursor (ec 4.99.1.1) (protoheme ferro-lyase) (heme synthetase). [source:swissprot;acc:p22830]	
3186	PRKCQ	protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [source:swissprot;acc:q04759]	
3187	DMRT3	doublesex and mab-3 related transcription factor 3; testis-specific protein; dmrt-like family a3. [source:refseq;acc:nm_021240]	
3188	WISP2	connective tissue growth factor-like protein precursor (ctgf-l) (wnt1 inducible signaling pathway protein 2) (wisp-2) (connective tissue growth factor-related protein 58). [source:swissprot;acc:o76076]	
3189	RNF4	ring finger protein 4. [source:swissprot;acc:p78317]	
3190	MTMR1	myotubularin-related protein 1 (ec 3.1.3.-). [source:swissprot;acc:q13613]	
3191	APPBP2	amyloid beta precursor protein-binding protein 2; amyloid beta precursor protein (cytoplasmic tail)-binding protein 2; protein interacting with app tail 1. [source:refseq;acc:nm_006380]	
3192	USP13	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). [source:swissprot;acc:q92995]	
3193	GDI2	rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [source:swissprot;acc:p50395]	
3194	MSH4	muts protein homolog 4. [source:swissprot;acc:o15457]	
3195	ITGB3	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [source:swissprot;acc:p05106]	
3196	HERPUD1	homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [source:swissprot;acc:q15011]	
3197	CLPTM1L	cisplatin resistance related protein crr9p. [source:refseq;acc:nm_030782]	
3198	DCUN1D1	rp42 homolog; squamous cell carcinoma-related oncogene. [source:refseq;acc:nm_020640]	
3199	C6	complement component c6 precursor. [source:swissprot;acc:p13671]	
3200	ZFYVE16	endosome-associated fyve-domain protein. [source:refseq;acc:nm_014733]	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/