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

Results: HTML CSV LaTeX

Showing element 1901 to 1950 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	Hugo	Value Type	red	network_comparison	green
238	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Divided	PPP1R7	Measured	27642.5	1.23182	22440.4
	rd protein. [swissprot;acc:p18615]		no value	Ranked	227.357	1.11785	254.15
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Subtracted	SNRPD3	Rooted	56.3709	9.524	65.8949
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]		STARD8	Measured	9649.61	1403.89	11053.5
239	adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109]		FDX1	Squared	36563.7	10407.4	46971.1
	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Divided	CPA6	Measured	7711.38	1.23071	6265.8
	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Subtracted	POLR2A	Ranked	243.817	24.145	267.962
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Divided	GSTO1		227.357	1.11785	254.15
	mad protein (max dimerizer). [swissprot;acc:q05195]	Subtracted	MXD1	Rooted	55.646	9.5074	65.1534
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Divided	no value		137.446	1.13758	120.823
	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]		MAPKAPK3	Squared	42411.6	1.31573	55802.1
	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]	Subtracted	CHRNA2	Measured	9649.61	1403.89	11053.5
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	Divided	AIG1	Ranked	227.357	1.11785	254.15
	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	Subtracted	RBBP4		252.39	24.093	228.297
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Divided	CPA3	Measured	7711.36	1.23071	6265.79
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Subtracted	MXI1	Rooted	55.6486	9.4992	65.1478
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Divided	MAGEA10		137.446	1.13758	120.823
	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]		MAPK14	Squared	42411.6	1.31573	55802.1
	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	Subtracted	MAPKAPK3	Measured	9649.61	1403.89	11053.5
	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]		UBE2E1	Squared	58831	10246.8	48584.2
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Divided	ATP5F1	Ranked	227.357	1.11785	254.15
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Subtracted	CDH1		241.892	24.068	265.96
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]		MXD4	Rooted	55.6495	9.4963	65.1458
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Divided	MAGEB4		137.446	1.13758	120.823
	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]	Subtracted	MAPK14	Measured	9649.61	1403.89	11053.5
	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Divided	CHRNA4	Squared	42411.6	1.31573	55802.1
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]		CPB2	Measured	7711.31	1.23071	6265.76
	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357]	Subtracted	UBE2E4P	Squared	58831	10246.8	48584.2
242	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]		no value	Ranked	241.892	24.067	265.959
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Divided	DNAJC12		227.357	1.11785	254.15
	kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719]	Subtracted	KYNU	Squared	35991.8	10011.1	46002.9
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]		RAB24	Rooted	55.65	9.4948	65.1448
	max protein. [swissprot;acc:p25912]	Divided	MAX	Measured	4640.26	1.22943	5704.87
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]		MAGED2	Rooted	137.446	1.13758	120.823
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]		CHRNA3	Squared	42411.6	1.31573	55802.1
	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Subtracted	CHRNA4	Measured	9649.61	1403.89	11053.5
243	60s ribosomal protein l23a. [swissprot;acc:p29316]		no value	Ranked	241.884	24.061	265.945
	dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442]		DRAP1	Squared	51805.2	9888.8	41916.4
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Divided	HOMER2	Measured	4246.95	1.22652	5208.98
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]	Subtracted	CHRNA3		9649.61	1403.89	11053.5
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]		PLDN	Rooted	63.1192	9.4648	72.584
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Divided	SNX13	Ranked	227.357	1.11785	254.15
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]		SPHK2	Squared	42411.6	1.31573	55802.1
	trophinin. [swissprot;acc:q12816]		TRO	Rooted	137.446	1.13758	120.823
244	60s ribosomal protein l5. [swissprot;acc:p46777]	Subtracted	RPL5	Ranked	241.899	24.025	265.924
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Divided	GSTO2		227.357	1.11785	254.15
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]		NCBP2L	Squared	14728.8	1.31245	19330.8
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]		MYO5B	Rooted	146.94	1.13683	167.046
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	Subtracted	NEUROD2		27.9136	9.3736	37.2872
	scratch; scratch 1. [refseq;acc:nm_031309]		no value	Squared	40388.9	9438.6	49827.5

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.