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

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

Results: HTML CSV LaTeX

Showing element 2708 to 2757 of 6456 in total

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

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison
1354	NDST3	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784]	Divided	228.409	223.475	1.02208
1355	LIAS	lipoic acid synthetase, mitochondrial (lip-syn) (lipoate synthase) (hussy-01) (fragment). [swissprot;acc:o43766]	Subtracted	204.961	209.517	4.556
	NDST4	n-deacetylase/n-sulfotransferase 4. [refseq;acc:nm_022569]	Divided	228.409	223.475	1.02208
1356	ATF7	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544]	Subtracted	218.667	214.118	4.549
	NDST1	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [swissprot;acc:p52848]	Divided	228.409	223.475	1.02208
1357	ATF2	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336]	Subtracted	218.657	214.11	4.547
	CDC27	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [swissprot;acc:p30260]	Divided	228.409	223.475	1.02208
1358	PGGT1B	geranylgeranyl transferase type i beta subunit (ec 2.5.1.-) (type i protein geranyl-geranyltransferase beta subunit) (ggtase-i-beta). [swissprot;acc:p53609]	Subtracted	225.039	229.573	4.534
	USF1	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	Divided	214.987	210.359	1.022
1359	FADS3	fatty acid desaturase 3; linoleoyl-coa desaturase (delta-6-desaturase)-like 3; delta-6 fatty acid desaturase. [refseq;acc:nm_021727]	Subtracted	225.039	229.573	4.534
	GSTT2B	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [swissprot;acc:p30712]	Divided	228.642	223.726	1.02197
1360	SMAD4	mothers against decapentaplegic homolog 4 (smad 4) (mothers against dpp homolog 4) (deletion target in pancreatic carcinoma 4) (hsmad4). [swissprot;acc:q13485]	Subtracted	225.039	229.573	4.534
	TGFBR1	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897]	Divided	223.89	228.805	1.02195
1361	FADS2	fatty acid desaturase 2; linoleoyl-coa desaturase (delta-6-desaturase)-like 2; delta-6 fatty acid desaturase. [refseq;acc:nm_004265]	Subtracted	225.039	229.573	4.534
	USF2	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853]	Divided	214.971	210.354	1.02195
1362	no value	fatty acid desaturase 1; linoleoyl-coa desaturase (delta-6-desaturase)-like 1; delta-5 desaturase; delta-5 fatty acid desaturase. [refseq;acc:nm_013402]	Subtracted	225.039	229.573	4.534
	PAOX	peroxisomal n1-acetyl-spermine/spermidine oxidase. [refseq;acc:nm_152911]	Divided	228.644	223.736	1.02194
1363	CREB5	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]		218.591	213.899
	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

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.