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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 77 to 126 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
77	CACNG2	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [source:swissprot;acc:q9y698]	254.692	202.668	1.2567	
78	CACNG8	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [source:swissprot;acc:q8wxs5]	254.693	202.668	1.2567	
79	CACNG3	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [source:swissprot;acc:o60359]	254.693	202.668	1.2567	
80	CACNG4	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [source:swissprot;acc:q9ubn1]	254.691	202.668	1.25669	
81	CACNG5	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [source:swissprot;acc:q9uf02]	254.614	202.646	1.25645	
82	GNB5	guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [source:swissprot;acc:o14775]	267.636	335.359	1.25304	
83	MAGED4	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [source:refseq;acc:nm_030801]	88.2482	110.265	1.24949	
84	MAGEE2	hepatocellular carcinoma-associated protein hca3. [source:refseq;acc:nm_138703]	88.2482	110.265	1.24949	
85		melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [source:swissprot;acc:p43357]	88.2482	110.265	1.24949	
86	MAGEA11	melanoma-associated antigen 11 (mage-11 antigen). [source:swissprot;acc:p43364]	88.2482	110.265	1.24949	
87	MAGEA2B	melanoma-associated antigen 2 (mage-2 antigen). [source:swissprot;acc:p43356]	88.2482	110.265	1.24949	
88		hepatocellular carcinoma-associated protein hca1. [source:refseq;acc:nm_020932]	88.2482	110.265	1.24949	
89	MAGEA6	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	88.2482	110.265	1.24949	
90	NDN	necdin. [source:swissprot;acc:q99608]	88.2482	110.265	1.24949	
91	MAGED1	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	88.2482	110.265	1.24949	
92	MAGEF1	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	88.2482	110.265	1.24949	
93	MAGEB6B	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	88.2482	110.265	1.24949	
94		melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	88.2482	110.265	1.24949	
95	MAGEA9	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	88.2482	110.265	1.24949	
96	MAGEA8	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	88.2482	110.265	1.24949	
97	MAGEC1	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	88.2482	110.265	1.24949	
98	MAGEA4	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	88.2482	110.265	1.24949	
99		melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	88.2482	110.265	1.24949	
100	MAGEA10	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	88.2482	110.265	1.24949	
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	

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/