Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.

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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 668 to 717 of 7460 in total

Value Type

: Measured
Interaction Map

: High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison
167	transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675]	Divided	0	331.61	417.983	1.26047
168	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Subtracted	1	4489.19	2765.82	1723.37
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Divided	1	23693.7	18263	1.29736
	serpin b12. [swissprot;acc:q96p63]	Subtracted	0	199.549	5.56738	193.982
	transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525]	Divided	0	334.012	420.355	1.2585
169	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Subtracted	1	4245.52	5942.75	1697.23
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Divided	0	244	194	1.25773
	hurpin (hacat uv-repressible serpin) (protease inhibitor 13) (headpin) (serpin b13). [swissprot;acc:q9uiv8]	Subtracted	0	199.249	5.71669	193.532
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Divided	1	23693.7	18263	1.29736
170	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Subtracted	0	668	475	193
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Subtracted	1	4247.86	5941.88	1694.02
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Divided	1	23693.7	18263	1.29736
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Divided	0	112.666	141.702	1.25772
171	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	Subtracted	0	594	402	192
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Subtracted	1	4117.67	5801.04	1683.37
	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]	Divided	1	23693.7	18263	1.29736
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	Divided	0	112.666	141.702	1.25772
172	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007]	Subtracted	1	4556.78	2945.26	1611.52
	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	Subtracted	0	1890.86	2081.91	191.05
	trophinin. [swissprot;acc:q12816]	Divided	1	23693.7	18263	1.29736
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]		0	112.666	141.702	1.25772
173	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]		1	4579.34	5940.64	1.29727
	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]		0	3265.25	4102.97	1.25656
	mesoderm induction early response 1. [refseq;acc:nm_020948]	Subtracted	0	1914.5	1723.5	191
	uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48]	Subtracted	1	4556.79	2945.28	1611.51
174	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	Divided	0	488.43	612.604	1.25423
	mad protein (max dimerizer). [swissprot;acc:q05195]	Divided	1	4455.95	5774.03	1.2958
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005]	Subtracted	1	4556.83	2945.38	1611.45
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	Subtracted	0	633.433	821.711	188.278
175	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	Divided		1382.5	1107	1.24887
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Subtracted		2056.14	2244.06	187.92
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Divided	1	4456.67	5773.77	1.29553
	serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4]	Subtracted	1	4556.99	2945.8	1611.19
176	40s ribosomal protein s29. [swissprot;acc:p30054]		0	1711.6	1895.38	183.78
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]		1	10235.2	11830.8	1595.6
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Divided	1	4456.93	5773.67	1.29544
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]		0	3023.85	2436.4	1.24111
177	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]		0	4131.06	3340.03	1.23683
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Subtracted	1	4110.14	5694.99	1584.85
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Divided	1	4457.06	5773.63	1.29539
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Subtracted	0	1124.15	943.423	180.727
178	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Divided		498.07	615.233	1.23523
	mstp028 protein. [refseq;acc:nm_031954]	Subtracted		9988.45	9808.48	179.97
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Divided	1	21591.5	27904.5	1.29238
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	Subtracted		10908.6	12491.8	1583.2
179	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Subtracted		4266.04	5843.51	1577.47
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Divided	0	556	681	1.22482
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Divided	1	21591.5	27904.5	1.29238
	ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916]	Subtracted	0	304.664	483.809	179.145
180	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596]	Subtracted	1	10872.4	12447	1574.6

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.

- http://analysis.yellowcouch.org/