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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1351 to 1400 of 3228 in total 
    Value Type	Ranked
    Network Comparison Type	Divided
    Interaction Map	High confidence
    Filtered	1
    
Rank	Hugo	description	red	green	network_comparison	
1351	PHB	prohibitin. [source:swissprot;acc:p35232]	211.513	206.941	1.02209	
1352		repressor of estrogen receptor activity; b-cell associated protein. [source:refseq;acc:nm_007273]	211.513	206.941	1.02209	
1353	NDST2	heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [source:swissprot;acc:p52849]	228.409	223.475	1.02208	
1354	NDST3	n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [source:refseq;acc:nm_004784]	228.409	223.475	1.02208	
1355	NDST4	n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569]	228.409	223.475	1.02208	
1356	NDST1	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [source:swissprot;acc:p52848]	228.409	223.475	1.02208	
1357	CDC27	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	228.409	223.475	1.02208	
1358	USF1	upstream stimulatory factor 1 (major late transcription factor 1). [source:swissprot;acc:p22415]	214.987	210.359	1.022	
1359	GSTT2B	glutathione s-transferase theta 2 (ec 2.5.1.18) (gst class-theta). [source:swissprot;acc:p30712]	228.642	223.726	1.02197	
1360	TGFBR1	tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [source:swissprot;acc:p36897]	223.89	228.805	1.02195	
1361	USF2	upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [source:swissprot;acc:q15853]	214.971	210.354	1.02195	
1362	PAOX	peroxisomal n1-acetyl-spermine/spermidine oxidase. [source:refseq;acc:nm_152911]	228.644	223.736	1.02194	
1363	CREB5	camp response element-binding protein cre-bpa. [source:refseq;acc:nm_004904]	218.591	213.899	1.02194	
1364	ACVR1B	serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [source:swissprot;acc:p36896]	223.885	228.797	1.02194	
1365	ATPIF1	atpase inhibitor, mitochondrial precursor. [source:swissprot;acc:q9uii2]	228.644	223.736	1.02194	
1366	ACVR1C	activin a receptor, type ic; activin receptor-like kinase 7. [source:refseq;acc:nm_145259]	223.884	228.795	1.02194	
1367	FREQ	neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [source:swissprot;acc:p36610]	223.887	228.799	1.02194	
1368	SMOX	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [source:refseq;acc:nm_019025]	228.644	223.736	1.02194	
1369	HCCS	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [source:swissprot;acc:p53701]	228.644	223.736	1.02194	
1370	NCK1	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [source:swissprot;acc:p16333]	205.185	200.784	1.02192	
1371	GSTT1	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [source:swissprot;acc:p30711]	228.646	223.744	1.02191	
1372	SOCS1	suppressor of cytokine signaling 1 (socs-1) (jak-binding protein) (jab) (stat induced stat inhibitor 1) (ssi-1) (tec-interacting protein 3) (tip-3). [source:swissprot;acc:o15524]	216.542	211.908	1.02187	
1373	GMFG	glia maturation factor gamma (gmf-gamma). [source:swissprot;acc:o60234]	216.542	211.908	1.02187	
1374	ASCC2	asc-1 complex subunit p100. [source:refseq;acc:nm_032204]	216.542	211.908	1.02187	
1375	FKBP1A	fk506-binding protein 1a (ec 5.2.1.8) (peptidyl-prolyl cis-trans isomerase) (ppiase) (rotamase) (12 kda fkbp) (fkbp-12) (immunophilin fkbp12). [source:swissprot;acc:p20071]	216.542	211.908	1.02187	
1376	EYA3	eyes absent homolog 3. [source:swissprot;acc:q99504]	218.537	213.91	1.02163	
1377	SALL2	sal-like protein 2 (zinc finger protein sall2) (hsal2). [source:swissprot;acc:q9y467]	218.471	213.876	1.02148	
1378	SALL3	sal-like protein 3 (zinc finger protein sall3) (hsall3). [source:swissprot;acc:q9bxa9]	218.47	213.876	1.02148	
1379	RERE	arginine-glutamic acid dipeptide (re) repeats; atrophin 1-like; arginine glutamic acid dipeptide re repeats. [source:refseq;acc:nm_012102]	218.47	213.875	1.02148	
1380	USP8	ubiquitin carboxyl-terminal hydrolase 8 (ec 3.1.2.15) (ubiquitin thiolesterase 8) (ubiquitin-specific processing protease 8) (deubiquitinating enzyme 8). [source:swissprot;acc:p40818]	218.47	213.876	1.02148	
1381	ROD1	rod1 regulator of differentiation 1; fission yeast differentiation regulator; regulator of differentiation (in s. pombi) 1; regulator of differentiation (in s. pombe) 1. [source:refseq;acc:nm_005156]	218.47	213.876	1.02148	
1382	PTBP2	polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [source:refseq;acc:nm_021190]	218.47	213.876	1.02148	
1383	AAK1	adaptor-associated kinase 1. [source:refseq;acc:nm_014911]	218.47	213.876	1.02148	
1384	ATN1	atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [source:swissprot;acc:p54259]	218.471	213.876	1.02148	
1385		dead (asp-glu-ala-asp) box polypeptide 47; hqp0256 protein. [source:refseq;acc:nm_016355]	218.47	213.875	1.02148	
1386	ARHGAP21	rho-gtpase activating protein 10. [source:refseq;acc:nm_020824]	218.47	213.876	1.02148	
1387	SALL1	sal-like protein 1 (zinc finger protein sall1) (spalt-like transcription factor 1) (hsal1). [source:swissprot;acc:q9nsc2]	218.47	213.875	1.02148	
1388	SALL4	sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	218.471	213.876	1.02148	
1389	BCKDHB	2-oxoisovalerate dehydrogenase beta subunit, mitochondrial precursor (ec 1.2.4.4) (branched-chain alpha-keto acid dehydrogenase e1 component beta chain) (bckdh e1-beta). [source:swissprot;acc:p21953]	218.47	213.875	1.02148	
1390	CNOT4	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [source:refseq;acc:nm_013316]	218.47	213.875	1.02148	
1391	PICALM	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	218.47	213.875	1.02148	
1392	SNAP91	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [source:swissprot;acc:o60641]	218.471	213.876	1.02148	
1393	RC3H2	membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835]	218.47	213.875	1.02148	
1394	PTBP1	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [source:swissprot;acc:p26599]	218.47	213.875	1.02148	
1395	GAS7	growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861]	218.47	213.876	1.02148	
1396	EYA1	eyes absent homolog 1. [source:swissprot;acc:q99502]	218.463	213.872	1.02147	
1397	RPS8	40s ribosomal protein s8. [source:swissprot;acc:p09058]	218.64	214.049	1.02145	
1398	EYA4	eyes absent homolog 4. [source:swissprot;acc:o95677]	218.449	213.864	1.02144	
1399	EYA2	eyes absent homolog 2. [source:swissprot;acc:o00167]	218.417	213.848	1.02137	
1400	ATF7	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544]	218.667	214.118	1.02125	

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/