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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 101 to 150 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
101	MAGEB4	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [source:swissprot;acc:p43366]	88.2482	110.265	1.24949	
102	MAGED2	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [source:swissprot;acc:q9unf1]	88.2482	110.265	1.24949	
103	TRO	trophinin. [source:swissprot;acc:q12816]	88.2482	110.265	1.24949	
104	HOMER2	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [source:refseq;acc:nm_004839]	252.371	202.016	1.24926	
105	GNB1	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [source:swissprot;acc:p04901]	266.716	333.165	1.24914	
106	COQ7	ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [source:swissprot;acc:q99807]	252.329	202.004	1.24913	
107	HOMER1	homer, neuronal immediate early gene, 1b. [source:refseq;acc:nm_004272]	252.309	201.998	1.24907	
108	HOMER3	homer, neuronal immediate early gene, 3. [source:refseq;acc:nm_004838]	252.296	201.995	1.24902	
109	GNB4	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [source:swissprot;acc:q9hav0]	266.933	333.281	1.24856	
110	DTX2	deltex 2. [source:refseq;acc:nm_020892]	333.144	267.393	1.2459	
111	DTX1	deltex homolog 1; hdx-1. [source:refseq;acc:nm_004416]	332.925	267.274	1.24563	
112	PBK	t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [source:refseq;acc:nm_018492]	332.874	267.246	1.24557	
113	KHDRBS3	kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [source:refseq;acc:nm_006558]	332.874	267.246	1.24557	
114	KHDRBS1	kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [source:refseq;acc:nm_006559]	332.874	267.246	1.24557	
115	KHDRBS2	kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [source:refseq;acc:nm_152688]	332.874	267.246	1.24557	
116	GNB3	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [source:swissprot;acc:p16520]	268.565	334.483	1.24545	
117	NEURL	neuralized-like. [source:refseq;acc:nm_004210]	332.326	266.948	1.24491	
118	NDUFA12	nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [source:swissprot;acc:q9ui09]	284.753	228.934	1.24382	
119	NDUFS4	nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [source:swissprot;acc:o43181]	318.982	259.004	1.23157	
120	KCND2	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [source:refseq;acc:nm_012281]	269.278	327.709	1.21699	
121	CTH	cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [source:swissprot;acc:p32929]	269.254	327.655	1.2169	
122	KCND3	potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [source:refseq;acc:nm_004980]	269.248	327.642	1.21688	
123	KCND1	potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [source:refseq;acc:nm_004979]	269.23	327.601	1.21681	
124	HMG20B	high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [source:refseq;acc:nm_006339]	208.52	171.595	1.21519	
125	HMG20A	high-mobility group 20a. [source:refseq;acc:nm_018200]	208.588	171.778	1.21429	
126	STAMBPL1	associated molecule with the sh3 domain of stam (amsh) like protein. [source:refseq;acc:nm_020799]	94	114	1.21277	
127	CHMP2A	putative breast adenocarcinoma marker (32kd). [source:refseq;acc:nm_014453]	94	114	1.21277	
128	STAMBP	associated molecule with the sh3 domain of stam. [source:refseq;acc:nm_006463]	94	114	1.21277	
129	VPS24	neuroendocrine differentiation factor; comparative gene identification transcript 149. [source:refseq;acc:nm_016079]	94	114	1.21277	
130	CHMP4A	protein hspc134 (protein cda04). [source:swissprot;acc:q9by43]	94	114	1.21277	
131	SON	son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [source:swissprot;acc:p18583]	294.053	242.562	1.21228	
132	TOB2	tob2 protein (transducer of erbb-2 2). [source:swissprot;acc:q14106]	350	290	1.2069	
133	TOB1	tob1 protein (transducer of erbb-2 1). [source:swissprot;acc:p50616]	350	290	1.2069	
134	DAB2IP	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [source:refseq;acc:nm_032552]	350	290	1.2069	
135	CPEB4	cytoplasmic polyadenylation element binding protein 4. [source:refseq;acc:nm_030627]	350	290	1.2069	
136	CPEB3	cytoplasmic polyadenylation element binding protein 3. [source:refseq;acc:nm_014912]	350	290	1.2069	
137	RASAL2	ras gtpase-activating protein ngap (ras protein activator like 1). [source:swissprot;acc:q9ujf2]	350	290	1.2069	
138	PPP2CA	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [source:swissprot;acc:p05323]	194.372	234.204	1.20493	
139	APBA1	amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [source:swissprot;acc:q02410]	271.752	225.68	1.20415	
140	RRAGA	ras-related gtp binding a; ras-related gtp-binding protein. [source:refseq;acc:nm_006570]	59	49	1.20408	
141	RRAGC	ras-related gtp binding c; rag c protein. [source:refseq;acc:nm_022157]	59	49	1.20408	
142	RRAGB	ras-related gtp binding b short isoform; gtp-binding protein ragb. [source:refseq;acc:nm_006064]	59	49	1.20408	
143	ANLN	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [source:refseq;acc:nm_018685]	59	49	1.20408	
144	KCNIP1	kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [source:refseq;acc:nm_014592]	265.686	319.651	1.20312	
145	KCNIP4	potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [source:refseq;acc:nm_147183]	265.639	319.546	1.20293	
146	KCNIP2	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]	265.632	319.531	1.20291	
147		nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	50.7983	42.3003	1.2009	
148	UNC84A	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	296.677	247.559	1.19841	
149		atlastin; guanylate-binding protein 3. [source:refseq;acc:nm_015915]	142	170	1.19718	
150	MYO5B	myosin vb (myosin 5b) (fragment). [source:swissprot;acc:q9ulv0]	55	46	1.19565	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/