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

Results: HTML CSV LaTeX

Showing element 1325 to 1374 of 66312 in total

Filtered  : 1

Rank	description	Hugo	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
83	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, beta isoform (pp2a, subunit a, pr65-beta isoform) (pp2a, subunit a, r1-beta isoform). [swissprot;acc:p30154]	PPP2R1B	Divided	Rooted	High confidence	63.6507	48.7127	1.30666
	set and mynd domain containing protein 1. [sptrembl;acc:q8nb12]	SMYD1	Subtracted		Low confidence	59.2532	66.0541	6.8009
	star-related lipid transfer protein 7 (stard7) (start domain- containing protein 7) (gtt1 protein). [swissprot;acc:q9nqz5]	STARD7	Divided			61.8872	67.9229	1.09753
			Subtracted	Ranked		228.743	210.764	17.979
84	amino acid transporter xat2; likely ortholog of mouse aspartate/glutamate transporter 1 (agt1). [refseq;acc:nm_138817]	SLC7A13		Rooted		68.7629	75.4877	6.7248
	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	BRAF	Divided	Squared	High confidence	117515	70412.3	1.66896
	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	CTBP1	Subtracted		Low confidence	82257.5	72122.5	10135
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	GNG3		Rooted	High confidence	40.3358	24.2919	16.0439
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	MAGEE2	Divided	Ranked		88.2482	110.265	1.24949
	homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838]	HOMER3	Subtracted			252.296	201.995	50.301
	jun dimerization protein. [refseq;acc:nm_130469]	no value	Divided	Measured		4932.27	7033.29	1.42597
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	MAGEB6B	Subtracted		Low confidence	11285.3	10318.5	966.8
	nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [swissprot;acc:q13952]	NFYC	Divided	Rooted	High confidence	46.7419	60.9337	1.30362
	nucleolin (protein c23). [swissprot;acc:p19338]	NCL		Squared	Low confidence	70162	58112.6	1.20735
	oligophrenin 1. [swissprot;acc:o60890]	OPHN1	Subtracted	Ranked		233.837	215.973	17.864
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	RRAGA		Squared	High confidence	103496	146848	43352
	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	SEPT4	Divided	Measured	Low confidence	11141.5	12351.1	1.10857
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	no value		Ranked		226.338	207.874	1.08882
				Rooted		62.4962	68.5193	1.09638
	type 1 protein phosphatase inhibitor. [refseq;acc:nm_025210]	PPP1R2P9	Subtracted	Measured	High confidence	21632.5	18090	3542.5
85	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	ATG12	Divided	Squared		67438.6	40697	1.65709
	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	BCL6	Subtracted		Low confidence	81993.8	71914	10079.8
	ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	NFYA	Divided	Rooted	High confidence	46.7419	60.9337	1.30362
	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	DFFB			Low confidence	61.1174	66.8946	1.09453
	fos-related antigen 2. [swissprot;acc:p15408]	FOSL2		Measured	High confidence	4941.95	7037.11	1.42395
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	GNG8	Subtracted	Rooted		40.336	24.2941	16.0419
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	no value	Divided	Ranked		88.2482	110.265	1.24949
	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]		Subtracted	Measured	Low confidence	11285.3	10318.5	966.8
	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]	ARHGAP26		Ranked		233.592	215.846	17.746
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	KCND2	Divided			225.735	245.308	1.08671
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	RRAGC	Subtracted	Squared	High confidence	103496	146848	43352
	ribosome biogenesis regulatory protein homolog. [swissprot;acc:q15050]	RRS1		Measured		21370.8	17896.5	3474.3
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	UNC84A		Ranked		296.677	247.559	49.118
	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641]	DVL2	Divided	Measured	Low confidence	7034.43	7797.14	1.10843
	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	no value		Squared		60862.1	50419.2	1.20712
	y+l amino acid transporter 1 (y(+)l-type amino acid transporter 1) (y+lat-1) (y+lat1) (monocyte amino acid permease 2) (mop-2). [swissprot;acc:q9um01]	SLC7A7	Subtracted	Rooted		68.7629	75.4877	6.7248
86	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	BCL6B		Squared		81989.8	71910.8	10079
	cystine/glutamate transporter (amino acid transport system xc-) (xct) (calcium channel blocker resistance protein ccbr1). [swissprot;acc:q9upy5]	SLC7A11		Rooted		68.7629	75.4877	6.7248
	dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8]	DGCR14		Ranked	High confidence	335	286	49
	dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075]	DFFB	Divided		Low confidence	233.922	215.309	1.08645
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	GNG5	Subtracted	Rooted	High confidence	40.3361	24.295	16.0411
	leucine zipper domain protein. [refseq;acc:nm_024589]	ROGDI		Ranked	Low confidence	221.996	238.82	16.824
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	MAGEA11	Divided		High confidence	88.2482	110.265	1.24949
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	MAGEA9	Subtracted	Measured	Low confidence	11285.3	10318.5	966.8
	protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	FOSB	Divided		High confidence	4942.49	7037.32	1.42384
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	RRAGB	Subtracted	Squared		103496	146848	43352
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	SEPT7	Divided		Low confidence	66860.1	80573.4	1.2051
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	PPP2R1A		Rooted	High confidence	63.6205	48.8838	1.30146
	serine/threonine protein phosphatase pp1-alpha 1 catalytic subunit (ec 3.1.3.16) (pp-1a). [swissprot;acc:p08129]	PPP1CA	Subtracted	Measured		21370.8	17896.5	3474.3
	transcription regulator protein bach1 (btb and cnc homolog 1) (ha2303). [swissprot;acc:o14867]	BACH1	Divided	Rooted	Low confidence	79.2778	86.7076	1.09372

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.