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

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 2725 to 2774 of 6456 in total

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

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison
1363	CREB5	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	Divided	218.591	213.899	1.02194
	NXF5	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Subtracted	168.989	164.46	4.529
1364	ACVR1B	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896]	Divided	223.885	228.797	1.02194
	NXF3	nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [swissprot;acc:q9h4d5]	Subtracted	168.995	164.467	4.528
1365	ATPIF1	atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]	Divided	228.644	223.736	1.02194
	NXF1	nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [swissprot;acc:q9ubu9]	Subtracted	169.031	164.507	4.524
1366	ACVR1C	activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259]	Divided	223.884	228.795	1.02194
	PRAF2	jm4 protein. [refseq;acc:nm_007213]	Subtracted	199.643	204.163	4.52
1367	ARL6IP5	cytoskeleton related vitamin a responsive protein; glutamate transporter eeac1-associated protein; dermal papilla derived protein 11; putative mapk activating protein pm27. [refseq;acc:nm_006407]		199.771	204.287	4.516
	FREQ	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610]	Divided	223.887	228.799	1.02194
1368	NPC2	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	Subtracted	205.204	200.71	4.494
	SMOX	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]	Divided	228.644	223.736	1.02194
1369	no value	cysteine-rich protein 1 (cysteine-rich intestinal protein) (crip) (cysteine-rich heart protein) (hcrhp). [swissprot;acc:p50238]	Subtracted	221.152	216.659	4.493
	HCCS	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]	Divided	228.644	223.736	1.02194
1370	CPSF4	cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	Subtracted	107.842	112.329	4.487
	NCK1	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	Divided	205.185	200.784	1.02192
1371	GSTT1	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711]		228.646	223.744	1.02191
	KIAA1012	trs85 homolog. [swissprot;acc:q9y2l5]	Subtracted	107.842	112.329	4.487
1372	ARAF	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]		129.913	134.399	4.486
	SOCS1	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [swissprot;acc:o15524]	Divided	216.542	211.908	1.02187
1373	GMFG	glia maturation factor gamma (gmf-gamma). [swissprot;acc:o60234]
	RAF1	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Subtracted	129.921	134.406	4.485
1374	ASCC2	asc-1 complex subunit p100. [refseq;acc:nm_032204]	Divided	216.542	211.908	1.02187
	WDR33	wd-repeat protein wdc146. [swissprot;acc:q9c0j8]	Subtracted	108.289	112.772	4.483
1375	CPSF1	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]
	FKBP1A	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [swissprot;acc:p20071]	Divided	216.542	211.908	1.02187
1376	EYA3	eyes absent homolog 3. [swissprot;acc:q99504]		218.537	213.91	1.02163
	RAD23A	uv excision repair protein rad23 homolog a (hhr23a). [swissprot;acc:p54725]	Subtracted	220.987	225.468	4.481
1377	PSMD4	26s proteasome non-atpase regulatory subunit 4 (26s proteasome regulatory subunit s5a) (rpn10) (multiubiquitin chain binding protein) (antisecretory factor-1) (af) (asf). [swissprot;acc:p55036]
	SALL2	sal-like protein 2 (zinc finger protein sall2) (hsal2). [swissprot;acc:q9y467]	Divided	218.471	213.876	1.02148
1378	OCRL	inositol polyphosphate 5-phosphatase ocrl-1 (ec 3.1.3.36) (lowe's oculocerebrorenal syndrome protein). [swissprot;acc:q01968]	Subtracted	220.987	225.468	4.481
	SALL3	sal-like protein 3 (zinc finger protein sall3) (hsall3). [swissprot;acc:q9bxa9]	Divided	218.47	213.876	1.02148
1379	RAD23B	uv excision repair protein rad23 homolog b (hhr23b) (xp-c repair complementing complex 58 kda protein) (p58). [swissprot;acc:p54727]	Subtracted	220.987	225.468	4.481
	RERE	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [refseq;acc:nm_012102]	Divided	218.47	213.875	1.02148
1380	no value	myosin vi. [swissprot;acc:q9um54]	Subtracted	220.987	225.468	4.481
	USP8	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [swissprot;acc:p40818]	Divided	218.47	213.876	1.02148
1381	MPP2	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	Subtracted	228.513	232.983	4.47
	ROD1	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [refseq;acc:nm_005156]	Divided	218.47	213.876	1.02148
1382	PPP2R5E	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	Subtracted	130.066	134.527	4.461
	PTBP2	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]	Divided	218.47	213.876	1.02148
1383	AAK1	adaptor-associated kinase 1. [refseq;acc:nm_014911]
	CCNG2	cyclin g2. [swissprot;acc:q16589]	Subtracted	130.066	134.527	4.461
1384	ATN1	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]	Divided	218.471	213.876	1.02148
	CCNG1	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Subtracted	130.066	134.527	4.461
1385	no value	dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [refseq;acc:nm_016355]	Divided	218.47	213.875	1.02148
	PPP2R5A	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	Subtracted	130.066	134.527	4.461
1386	ARHGAP21	rho-gtpase activating protein 10. [refseq;acc:nm_020824]	Divided	218.47	213.876	1.02148
	TNPO3	transportin-sr; importin 12. [refseq;acc:nm_012470]	Subtracted	225.305	229.766	4.461
1387	BOLA2B	my016 protein. [sptrembl;acc:q9h3k6]		224.755	229.2	4.445
	SALL1	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [swissprot;acc:q9nsc2]	Divided	218.47	213.875	1.02148

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.