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

Results: HTML CSV LaTeX

Showing element 2780 to 2829 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
1390	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316]	Divided	218.47	213.875	1.02148
1391	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492]
	sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637]	Subtracted	214.717	219.157	4.44
1392	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]	Divided	218.471	213.876	1.02148
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Subtracted	214.717	219.157	4.44
1393	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]		130.289	134.713	4.424
	membrane-associated nucleic acid binding protein. [refseq;acc:nm_018835]	Divided	218.47	213.875	1.02148
1394	caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [swissprot;acc:o75844]	Subtracted	226.532	222.117	4.415
	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]	Divided	218.47	213.875	1.02148
1395	growth-arrest-specific protein 7 (gas-7). [swissprot;acc:o60861]			213.876
	heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [swissprot;acc:p04792]	Subtracted	221.817	226.23	4.413
1396	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]		205.185	200.784	4.401
	eyes absent homolog 1. [swissprot;acc:q99502]	Divided	218.463	213.872	1.02147
1397	40s ribosomal protein s8. [swissprot;acc:p09058]		218.64	214.049	1.02145
	alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [swissprot;acc:q9ujy1]	Subtracted	221.804	226.194	4.39
1398	eyes absent homolog 4. [swissprot;acc:o95677]	Divided	218.449	213.864	1.02144
	wd repeat domain 26. [refseq;acc:nm_025160]	Subtracted	213.351	217.74	4.389
1399	eyes absent homolog 2. [swissprot;acc:o00167]	Divided	218.417	213.848	1.02137
	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5]	Subtracted	228.469	232.855	4.386
1400	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544]	Divided	218.667	214.118	1.02125
	proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903]	Subtracted	170.28	165.898	4.382
1401	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336]	Divided	218.657	214.11	1.02124
	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	Subtracted	212.833	208.456	4.377
1402	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	Divided	209.682	205.329	1.0212
		Subtracted			4.353
1403	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]		110.2	114.552	4.352
	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [swissprot;acc:p30084]	Divided	184.656	180.823	1.0212
1404	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	Subtracted	242.181	237.834	4.347
	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427]	Divided	232.752	237.65	1.02104
1405	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]		245.532	240.483	1.021
	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_145245]	Subtracted	218.829	214.493	4.336
1406	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [refseq;acc:nm_005665]
	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406]	Divided	212.833	208.456	1.021
1407	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]		206.104	210.424	1.02096
		Subtracted			4.32
1408	stromal interaction molecule 1 precursor. [swissprot;acc:q13586]	Divided	206.102	210.42	1.02095
		Subtracted			4.318
1409	trap/mediator complex component trap25. [refseq;acc:nm_080651]	Divided			1.02095
		Subtracted			4.318
1410	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]
	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	Divided	206.1	210.417	1.02095
1411	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	Subtracted	206.102	210.42	4.318
	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]	Divided			1.02095
1412	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]	Subtracted			4.318
	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	Divided			1.02095
1413	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Subtracted			4.318
1414		Divided			1.02095
	stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]	Subtracted			4.318
1415	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]

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.