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 5908 to 5957 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	green	network_comparison
1477	transformer-2 protein homolog (tra-2 alpha). [swissprot;acc:q13595]	Ranked	215.328	211.267	1.01922
1478	arginine/serine-rich splicing factor 10 (transformer-2-beta) (htra2- beta) (transformer 2 protein homolog) (silica-induced protein 41) (ra301). [swissprot;acc:q15815]		215.122	211.066
	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544]	Measured	5659.22	6084.68	1.07518
	integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287]	Rooted	65.7121	68.2158	1.0381
	ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]	Squared	26860.7	29969	1.11572
1479	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	Measured	5787.03	6221.72	1.07511
	integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]	Rooted	65.7121	68.2158	1.0381
	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5]	Ranked	228.469	232.855	1.0192
	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]	Squared	26860.7	29969	1.11572
1480	cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007]	Ranked	218.664	214.55	1.01918
	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336]	Measured	5660.17	6085.22	1.07509
	dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514]	Squared	15124.2	16872.9	1.11562
	integral membrane protein 2a (e25 protein). [swissprot;acc:o43736]	Rooted	65.7121	68.2158	1.0381
1481	26s protease regulatory subunit 7 (mss1 protein). [swissprot;acc:p35998]	Squared	26142.6	29163.8	1.11557
	cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661]	Ranked	208.432	204.516	1.01915
	egf-like-domain, multiple 7; neu1 protein. [refseq;acc:nm_016215]	Measured	3688.8	3431.33	1.07504
	mitogen-activated protein kinase kinase kinase 7 interacting protein 1 (tak1-binding protein 1). [swissprot;acc:q15750]	Rooted	63.582	66.002	1.03806
1482	enigma protein; lim domain protein. [refseq;acc:nm_005451]		61.1844	63.5127	1.03805
	leng5 protein. [refseq;acc:nm_024075]	Measured	5372.25	5775.21	1.07501
	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	Ranked	224.354	220.15	1.0191
	protein bap28. [swissprot;acc:q9h583]	Squared	14997.9	16728.4	1.11538
1483	cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639]		31810.3	35473.9	1.11517
	eukaryotic translation initiation factor 3 subunit 7 (eif-3 zeta) (eif3 p66) (eif3d). [swissprot;acc:o15371]	Rooted	61.1844	63.5127	1.03805
	pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177]	Ranked	198.927	202.726	1.0191
	tryptophanyl-trna synthetase (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) (ifp53) (hwrs). [swissprot;acc:p23381]	Measured	5372.25	5775.21	1.07501
1484	2-oxoisovalerate dehydrogenase alpha subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component alpha chain) (bckdh e1-alpha). [swissprot;acc:p12694]	Ranked	198.927	202.726	1.0191
	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	Squared	22974.7	25619.9	1.11514
	evolutionarily conserved signaling intermediate in toll pathway; ecsit. [refseq;acc:nm_016581]	Rooted	64.2463	66.6861	1.03798
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Measured	5372.25	5775.21	1.07501
1485	chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	Squared	26696.5	29768.6	1.11508
	j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330]	Ranked	207.877	203.989	1.01906
	methionyl-trna formyltransferase, mitochondrial precursor (ec 2.1.2.9) (mtfmt). [swissprot;acc:q96dp5]	Rooted	59.2072	61.4511	1.0379
	tryptophanyl-trna synthetase, mitochondrial precursor (ec 6.1.1.2) (tryptophan--trna ligase) (trprs) ((mt)trprs). [swissprot;acc:q9ugm6]	Measured	5372.25	5775.21	1.07501
1486	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	Rooted	79.3006	82.3013	1.03784
	human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]	Ranked	207.877	203.989	1.01906
	kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9]	Squared	26696.5	29768.6	1.11508
	thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445]	Measured	5372.25	5775.21	1.07501
1487	conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746]	Squared	26696.5	29768.6	1.11508
	dual specificity mitogen-activated protein kinase kinase 1 (ec 2.7.1.-) (map kinase kinase 1) (mapkk 1) (erk activator kinase 1) (mapk/erk kinase 1) (mek1). [swissprot;acc:q02750]	Rooted	62.3212	64.678	1.03782
	nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [refseq;acc:nm_178177]	Measured	5573.64	5991.58	1.07499
	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]	Ranked	207.877	203.989	1.01906
1488	delta 1-pyrroline-5-carboxylate synthetase (p5cs) [includes: glutamate 5-kinase (ec 2.7.2.11) (gamma-glutamyl kinase) (gk); gamma-glutamyl phosphate reductase (gpr) (ec 1.2.1.41) (glutamate-5-semialdehyde dehydrogenase) (glutamyl-gamma-semialdehyde dehydrogenase)]. [swissprot;acc:p54886]	Measured	5573.64	5991.58	1.07499
	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	Ranked	207.877	203.989	1.01906
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	Squared	26696.5	29768.6	1.11508
	similar to kinase suppressor of ras (fragment). [sptrembl;acc:q8ivt5]	Rooted	62.3212	64.678	1.03782
1489	26s protease regulatory subunit 6b (mip224) (mb67 interacting protein) (tat-binding protein-7) (tbp-7). [swissprot;acc:p43686]	Squared	26277.3	29299.3	1.115
	dual specificity mitogen-activated protein kinase kinase 2 (ec 2.7.1.-) (map kinase kinase 2) (mapkk 2) (erk activator kinase 2) (mapk/erk kinase 2) (mek2). [swissprot;acc:p36507]	Rooted	62.3212	64.678	1.03782
	mitogen-activated protein kinase kinase kinase 7 (ec 2.7.1.-) (transforming growth factor-beta-activated kinase 1) (tgf-beta- activated kinase 1). [swissprot;acc:o43318]	Ranked	213.251	209.264	1.01905
	vesicle-fusing atpase (ec 3.6.4.6) (vesicular-fusion protein nsf) (n- ethylmaleimide sensitive fusion protein) (nem-sensitive fusion protein). [swissprot;acc:p46459]	Measured	6192.38	6656.34	1.07492
1490	f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907]		6340.5	6815.41	1.0749

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.