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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1808 to 1857 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
1808	lysyl-trna synthetase (ec 6.1.1.6) (lysine--trna ligase) (lysrs). [source:swissprot;acc:q15046]	4941.92	5265.09	1.06539	
1809	epsin 3. [source:refseq;acc:nm_017957]	5816.12	6196.21	1.06535	
1810	colorectal mutant cancer protein (mcc protein). [source:swissprot;acc:p23508]	6520.83	6946.75	1.06532	
1811	tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [source:refseq;acc:nm_015975]	7659.42	8156.79	1.06494	
1812	hrd1 protein isoform a; synoviolin1. [source:refseq;acc:nm_032431]	5514.19	5871.64	1.06482	
1813	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [source:swissprot;acc:p45985]	5866.19	6245.4	1.06464	
1814	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [source:swissprot;acc:p08238]	5733.71	6104.26	1.06463	
1815	junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [source:swissprot;acc:q9y624]	6104.77	6498.84	1.06455	
1816	potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [source:refseq;acc:nm_020122]	5633.44	5997	1.06454	
1817	solute carrier family 23, member 1 (sodium-dependent vitamin c transporter 1) (hsvct1) (na(+)/l-ascorbic acid transporter 1) (yolk sac permease-like molecule 3). [source:swissprot;acc:q9uhi7]	5633.44	5997	1.06454	
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	

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/