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 1818 to 1867 of 3228 in total

Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1818	heterogeneous nuclear ribonucleoprotein a3 (hnrnp a3) (d10s102). [source:swissprot;acc:p51991]	5633.44	5997	1.06454	
1819	adp-ribosylation factor 4. [source:swissprot;acc:p18085]	5633.44	5997	1.06454	
1820	fused toes homolog; likely ortholog of mouse fused toes. [source:refseq;acc:nm_022476]	5633.44	5997	1.06454	
1821	shc transforming protein. [source:swissprot;acc:p29353]	5633.44	5997	1.06454	
1822	zinc finger protein 289, id1 regulated; likely ortholog of mouse zfp289. [source:refseq;acc:nm_032389]	5633.44	5997	1.06454	
1823	neuronal shc. [source:refseq;acc:nm_016848]	5633.44	5997	1.06454	
1824	adp-ribosylation factor 1. [source:swissprot;acc:p32889]	5633.44	5997	1.06454	
1825	heterogeneous nuclear ribonucleoprotein a1 (helix-destabilizing protein) (single-strand binding protein) (hnrnp core protein a1). [source:swissprot;acc:p09651]	5633.44	5997	1.06454	
1826	adp-ribosylation factor 3. [source:swissprot;acc:p16587]	5633.44	5997	1.06454	
1827	protein sck (fragment). [source:swissprot;acc:p98077]	5633.44	5997	1.06454	
1828	heterogeneous nuclear ribonucleoproteins a2/b1 (hnrnp a2 / hnrnp b1). [source:swissprot;acc:p22626]	5633.44	5997	1.06454	
1829	ovarian carcinoma immunoreactive antigen. [source:refseq;acc:nm_017830]	5633.44	5997	1.06454	
1830	adp-ribosylation factor gtpase-activating protein 3 (arf gap 3). [source:swissprot;acc:q9np61]	5633.44	5997	1.06454	
1831	solute carrier family 23, member 2 (sodium-dependent vitamin c transporter 2) (hsvct2) (na(+)/l-ascorbic acid transporter 2) (yolk sac permease-like molecule 2) (nucleobase transporter-like 1 protein). [source:swissprot;acc:q9ugh3]	5633.44	5997	1.06454	
1832	dual specificity mitogen-activated protein kinase kinase 7 (ec 2.7.1.-) (map kinase kinase 7) (mapkk 7) (mapk/erk kinase 7) (jnk activating kinase 2) (c-jun n-terminal kinase kinase 2) (jnk kinase 2) (jnkk 2). [source:swissprot;acc:o14733]	5633.44	5997	1.06454	
1833	5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [source:swissprot;acc:p49914]	6175.23	6572.85	1.06439	
1834	60s ribosomal protein l11. [source:swissprot;acc:p39026]	3593.24	3375.93	1.06437	
1835	transcription elongation factor a protein 2 (transcription elongation factor s-ii protein 2) (testis-specific s-ii) (transcription elongation factor tfiis.l). [source:swissprot;acc:q15560]	5019.3	5342.36	1.06436	
1836	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [source:swissprot;acc:p23193]	5019.3	5342.36	1.06436	
1837	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [source:refseq;acc:nm_002873]	5739.49	6108.72	1.06433	
1838	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). [source:swissprot;acc:p12956]	5739.49	6108.72	1.06433	
1839	atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [source:swissprot;acc:p13010]	5739.49	6108.72	1.06433	
1840	cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [source:swissprot;acc:p49585]	3591.95	3375.34	1.06417	
1841	fad synthetase. [source:refseq;acc:nm_025207]	3591.95	3375.34	1.06417	
1842	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o95340]	3591.95	3375.34	1.06417	
1843	ligatin (hepatocellular carcinoma-associated antigen 56). [source:swissprot;acc:p41214]	3591.95	3375.34	1.06417	
1844	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [source:swissprot;acc:o43252]	3591.95	3375.34	1.06417	
1845	nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [source:swissprot;acc:p16435]	3591.95	3375.34	1.06417	
1846	cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [source:swissprot;acc:q9y5k3]	3591.95	3375.34	1.06417	
1847	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [source:swissprot;acc:p15104]	6215.55	6613.46	1.06402	
1848	heat shock protein hsp 90-alpha (hsp 86). [source:swissprot;acc:p07900]	5746.06	6113.79	1.064	
1849	arginase ii, mitochondrial precursor (ec 3.5.3.1) (non-hepatic arginase) (kidney-type arginase). [source:swissprot;acc:p78540]	6267.93	6668.72	1.06394	
1850	protein kinase c binding protein 1 (rack7) (cutaneous t-cell lymphoma associated antigen se14-3) (ctcl tumor antigen se14-3) (zinc finger mynd domain containing protein 8). [source:swissprot;acc:q9ulu4]	6158.6	6551.94	1.06387	
1851	adenovirus 5 e1a-binding protein (bs69 protein). [source:swissprot;acc:q15326]	6156.28	6549.03	1.0638	
1852	arginase 1 (ec 3.5.3.1) (liver-type arginase). [source:swissprot;acc:p05089]	6271.17	6670.97	1.06375	
1853	keratin associated protein 9.2. [source:refseq;acc:nm_031961]	6076.65	6463.64	1.06368	
1854	keratin associated protein 4-10; keratin associated protein 4.10. [source:refseq;acc:nm_033060]	6076.66	6463.14	1.0636	
1855	keratin associated protein 4-2; keratin associated protein 4.2. [source:refseq;acc:nm_033062]	6076.66	6463.14	1.0636	
1856	keratin associated protein 4.3 (fragment). [source:sptrembl;acc:q9byr4]	6076.66	6463.14	1.0636	
1857	keratin associated protein 2-4; keratin associated protein 2.4. [source:refseq;acc:nm_033184]	6076.66	6463.15	1.0636	
1858	keratin associated protein 4-14; keratin associated protein 4.14. [source:refseq;acc:nm_033059]	6076.66	6463.13	1.0636	
1859	keratin associated protein 4.9 (fragment). [source:sptrembl;acc:q9byq8]	6076.66	6463.13	1.0636	
1860	keratin associated protein 4-12; keratin associated protein 4.12. [source:refseq;acc:nm_031854]	6076.66	6463.13	1.0636	
1861	keratin associated protein 1.5. [source:refseq;acc:nm_031957]	6076.66	6463.14	1.0636	
1862	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [source:swissprot;acc:p59095]	6076.66	6463.13	1.0636	
1863	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [source:swissprot;acc:o75690]	6076.66	6463.14	1.0636	
1864	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [source:swissprot;acc:p26371]	6076.66	6463.14	1.0636	
1865	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [source:swissprot;acc:q9nsy2]	6076.66	6463.12	1.0636	
1866	keratin associated protein 4.4. [source:refseq;acc:nm_032524]	6076.66	6463.14	1.0636	
1867	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [source:swissprot;acc:q9nvd7]	6076.66	6463.12	1.0636	

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/