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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1794 to 1843 of 3228 in total

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

Rank	description	red	green	network_comparison	
1794	epsin 2 isoform b; eps15 binding protein. [source:refseq;acc:nm_014964]	5948.26	6342.84	1.06634	
1795	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [source:swissprot;acc:q9y2y1]	5501.3	5866.02	1.0663	
1796	tubulin tyrosine ligase-like protein hottl (hqp0207). [source:swissprot;acc:q9y4r7]	5387.64	5743.5	1.06605	
1797	valyl-trna synthetase 2 (ec 6.1.1.9) (valine--trna ligase 2) (valrs 2) (g7a). [source:swissprot;acc:p26640]	5096.02	5432.63	1.06605	
1798	60s ribosomal protein l32. [source:swissprot;acc:p02433]	3618.02	3394.29	1.06591	
1799	translation initiation factor eif-2b beta subunit (eif-2b gdp-gtp exchange factor) (s20i15) (s20iii15). [source:swissprot;acc:p49770]	5456.57	5816.14	1.0659	
1800	translation initiation factor eif-2b delta subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q9ui10]	5424.3	5781.58	1.06587	
1801	epsin 1; eh domain-binding mitotic phosphoprotein. [source:refseq;acc:nm_013333]	5881.33	6268.57	1.06584	
1802	thymidylate synthase (ec 2.1.1.45) (ts) (tsase). [source:swissprot;acc:p04818]	4980.54	5307.81	1.06571	
1803	dihydrofolate reductase (ec 1.5.1.3). [source:swissprot;acc:p00374]	4980.54	5307.81	1.06571	
1804	stromal cell-derived factor 2 precursor (sdf-2). [source:swissprot;acc:q99470]	4980.54	5307.81	1.06571	
1805	stromal cell-derived factor 2-like protein 1 precursor (sdf2 like protein 1) (pwp1-interacting protein 8). [source:swissprot;acc:q9hcn8]	4980.54	5307.81	1.06571	
1806	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [source:swissprot;acc:p14618]	4783.49	5097.66	1.06568	
1807	endothelial-derived gene 1. [source:refseq;acc:nm_025205]	6399.54	6818.17	1.06542	
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	

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/