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 1277 to 1326 of 25824 in total

Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison	
160	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	Rooted	Subtracted	43.4291	31.7159	11.7132	
160	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Measured	Divided	23693.7	18263	1.29736	
160	neurogenic differentiation factor 6 (neurod6) (my051 protein). [source:swissprot;acc:q96nk8]	Ranked	Subtracted	312	284	28	
160	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	Squared	Subtracted	42788.3	60162.6	17374.3	
161	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Squared	Divided	173408	242989	1.40126	
161	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Measured	Divided	23693.7	18263	1.29736	
161	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Measured	Subtracted	9035	7279.6	1755.4	
161	neurogenic differentiation factor 1 (neurod1) (neurod). [source:swissprot;acc:q13562]	Ranked	Subtracted	312	284	28	
161	ns1-associated protein 1. [source:refseq;acc:nm_006372]	Rooted	Divided	52.7642	61.9019	1.17318	
161	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	Rooted	Subtracted	43.4519	31.7522	11.6997	
161	rap1 gtpase-activating protein 1 (rap1gap). [source:swissprot;acc:p47736]	Ranked	Divided	249.663	298.263	1.19466	
161	trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [source:swissprot;acc:o75648]	Squared	Subtracted	52591.3	69845.1	17253.8	
162	atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	Ranked	Subtracted	142	170	28	
162	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [source:swissprot;acc:o43390]	Rooted	Divided	52.7642	61.9019	1.17318	
162	high-mobility group 20a. [source:refseq;acc:nm_018200]	Measured	Subtracted	5140.14	6893.53	1753.39	
162	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Squared	Divided	173408	242989	1.40126	
162	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [source:refseq;acc:nm_173193]	Rooted	Subtracted	43.4554	31.7576	11.6978	
162	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Measured	Divided	23693.7	18263	1.29736	
162	nostrin. [source:refseq;acc:nm_052946]	Ranked	Divided	209.299	249.187	1.19058	
162	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [source:refseq;acc:nm_002975]	Squared	Subtracted	59704	76460.4	16756.4	
163	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [source:swissprot;acc:p52298]	Rooted	Subtracted	54.935	66.6101	11.6751	
163	beta-arrestin 2 (arrestin, beta 2). [source:swissprot;acc:p32121]	Ranked	Subtracted	133	105	28	
163	c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [source:swissprot;acc:o75596]	Squared	Subtracted	59464	76120.8	16656.8	
163	eap30 subunit of ell complex. [source:refseq;acc:nm_007241]	Ranked	Divided	209.299	249.187	1.19058	
163	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [source:swissprot;acc:q04637]	Rooted	Divided	52.7702	61.8915	1.17285	
163	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Squared	Divided	173408	242989	1.40126	
163	likely ortholog of mouse variant polyadenylation protein cstf-64. [source:refseq;acc:nm_015235]	Measured	Subtracted	14976.4	13246.6	1729.8	
163	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Measured	Divided	23693.7	18263	1.29736	
164	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [source:swissprot;acc:q04446]	Measured	Subtracted	4489.19	2765.82	1723.37	
164	beta-arrestin 1 (arrestin, beta 1). [source:swissprot;acc:p49407]	Ranked	Subtracted	133	105	28	
164	deoxyuridine 5'-triphosphate nucleotidohydrolase, mitochondrial precursor (ec 3.6.1.23) (dutpase) (dutp pyrophosphatase). [source:swissprot;acc:p33316]	Squared	Subtracted	61733.5	45224.1	16509.4	
164	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Squared	Divided	173408	242989	1.40126	
164	liv-1 protein, estrogen regulated. [source:refseq;acc:nm_012319]	Ranked	Divided	209.299	249.187	1.19058	
164	mad protein (max dimerizer). [source:swissprot;acc:q05195]	Rooted	Divided	55.646	65.1534	1.17086	
164	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Measured	Divided	23693.7	18263	1.29736	
164	musashi 2 isoform a. [source:refseq;acc:nm_138962]	Rooted	Subtracted	54.9787	66.2416	11.2629	
165	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [source:swissprot;acc:q05329]	Ranked	Divided	209.299	249.187	1.19058	
165	glycogen phosphorylase, brain form (ec 2.4.1.1). [source:swissprot;acc:p11216]	Measured	Subtracted	4489.19	2765.82	1723.37	
165	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Squared	Divided	173408	242989	1.40126	
165	max interacting protein 1 (mxi1 protein). [source:swissprot;acc:p50539]	Rooted	Divided	55.6486	65.1478	1.1707	
165	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Measured	Divided	23693.7	18263	1.29736	
165	musashi 1. [source:refseq;acc:nm_002442]	Rooted	Subtracted	54.9787	66.2416	11.2629	
165	spermatogenesis associated 6. [source:refseq;acc:nm_019073]	Ranked	Subtracted	133	105	28	
165	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	Squared	Subtracted	59016.1	75486.9	16470.8	
166	c-terminal binding protein 2 (ctbp2). [source:swissprot;acc:p56545]	Squared	Subtracted	69201.8	53013.4	16188.4	
166	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [source:swissprot;acc:q99747]	Ranked	Divided	209.299	249.187	1.19058	
166	glycogen phosphorylase, liver form (ec 2.4.1.1). [source:swissprot;acc:p06737]	Measured	Subtracted	4489.19	2765.82	1723.37	
166	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Squared	Divided	173408	242989	1.40126	
166	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [source:swissprot;acc:q14582]	Rooted	Divided	55.6495	65.1458	1.17064	
166	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Measured	Divided	23693.7	18263	1.29736	

Legend:
- Rank is the rank after comparing the two networks
- 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/