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.


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 2775 to 2824 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
1388	sal-like protein 4 (zinc finger protein sall4). [source:swissprot;acc:q9ujq4]	Divided	218.471	213.876	1.02148	
1388	sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [source:swissprot;acc:p05023]	Subtracted	214.717	219.157	4.44	
1389	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]	Divided	218.47	213.875	1.02148	
1389	cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [source:swissprot;acc:o60911]	Subtracted	214.717	219.157	4.44	
1390	cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [source:swissprot;acc:p07711]	Subtracted	214.717	219.157	4.44	
1390	ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [source:refseq;acc:nm_013316]	Divided	218.47	213.875	1.02148	
1391	phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [source:swissprot;acc:q13492]	Divided	218.47	213.875	1.02148	
1391	sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [source:swissprot;acc:p13637]	Subtracted	214.717	219.157	4.44	
1392	clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [source:swissprot;acc:o60641]	Divided	218.471	213.876	1.02148	
1392	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [source:swissprot;acc:p50993]	Subtracted	214.717	219.157	4.44	
1393	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Subtracted	130.289	134.713	4.424	
1393	membrane-associated nucleic acid binding protein. [source:refseq;acc:nm_018835]	Divided	218.47	213.875	1.02148	
1394	caax prenyl protease 1 homolog (ec 3.4.24.-) (prenyl protein-specific endoprotease 1) (farnesylated-proteins converting enzyme 1) (face-1) (zinc metalloproteinase ste24 homolog). [source:swissprot;acc:o75844]	Subtracted	226.532	222.117	4.415	
1394	polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [source:swissprot;acc:p26599]	Divided	218.47	213.875	1.02148	
1395	growth-arrest-specific protein 7 (gas-7). [source:swissprot;acc:o60861]	Divided	218.47	213.876	1.02148	
1395	heat shock 27 kda protein (hsp 27) (stress-responsive protein 27) (srp27) (estrogen-regulated 24 kda protein) (28 kda heat shock protein). [source:swissprot;acc:p04792]	Subtracted	221.817	226.23	4.413	
1396	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [source:swissprot;acc:p16333]	Subtracted	205.185	200.784	4.401	
1396	eyes absent homolog 1. [source:swissprot;acc:q99502]	Divided	218.463	213.872	1.02147	
1397	40s ribosomal protein s8. [source:swissprot;acc:p09058]	Divided	218.64	214.049	1.02145	
1397	alpha crystallin c chain (small stress protein-like protein hsp22) (e2ig1) (protein kinase h11). [source:swissprot;acc:q9ujy1]	Subtracted	221.804	226.194	4.39	
1398	eyes absent homolog 4. [source:swissprot;acc:o95677]	Divided	218.449	213.864	1.02144	
1398	wd repeat domain 26. [source:refseq;acc:nm_025160]	Subtracted	213.351	217.74	4.389	
1399	eyes absent homolog 2. [source:swissprot;acc:o00167]	Divided	218.417	213.848	1.02137	
1399	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [source:swissprot;acc:q9nzw5]	Subtracted	228.469	232.855	4.386	
1400	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [source:swissprot;acc:p17544]	Divided	218.667	214.118	1.02125	
1400	proline synthetase co-transcribed bacterial homolog protein. [source:swissprot;acc:o94903]	Subtracted	170.28	165.898	4.382	
1401	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [source:swissprot;acc:p15336]	Divided	218.657	214.11	1.02124	
1401	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	Subtracted	212.833	208.456	4.377	
1402	colorectal mutant cancer protein (mcc protein). [source:swissprot;acc:p23508]	Divided	209.682	205.329	1.0212	
1402	colorectal mutant cancer protein (mcc protein). [source:swissprot;acc:p23508]	Subtracted	209.682	205.329	4.353	
1403	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [source:swissprot;acc:q9p2i0]	Subtracted	110.2	114.552	4.352	
1403	enoyl-coa hydratase, mitochondrial precursor (ec 4.2.1.17) (short chain enoyl-coa hydratase) (sceh) (enoyl-coa hydratase 1). [source:swissprot;acc:p30084]	Divided	184.656	180.823	1.0212	
1404	hiv-1 rev binding protein 2; rev interacting protein. [source:refseq;acc:nm_007043]	Subtracted	242.181	237.834	4.347	
1404	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [source:swissprot;acc:q15427]	Divided	232.752	237.65	1.02104	
1405	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	Divided	245.532	240.483	1.021	
1405	similar to ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_145245]	Subtracted	218.829	214.493	4.336	
1406	ecotropic viral integration site 5; neuroblastoma stage 4s gene. [source:refseq;acc:nm_005665]	Subtracted	218.829	214.493	4.336	
1406	orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	Divided	212.833	208.456	1.021	
1407	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [source:refseq;acc:nm_020830]	Divided	206.104	210.424	1.02096	
1407	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [source:refseq;acc:nm_020830]	Subtracted	206.104	210.424	4.32	
1408	stromal interaction molecule 1 precursor. [source:swissprot;acc:q13586]	Divided	206.102	210.42	1.02095	
1408	stromal interaction molecule 1 precursor. [source:swissprot;acc:q13586]	Subtracted	206.102	210.42	4.318	
1409	trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	Divided	206.102	210.42	1.02095	
1409	trap/mediator complex component trap25. [source:refseq;acc:nm_080651]	Subtracted	206.102	210.42	4.318	
1410	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [source:swissprot;acc:o96013]	Subtracted	206.102	210.42	4.318	
1410	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [source:refseq;acc:nm_052950]	Divided	206.1	210.417	1.02095	
1411	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	Subtracted	206.102	210.42	4.318	
1411	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [source:swissprot;acc:o96013]	Divided	206.102	210.42	1.02095	
1412	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [source:swissprot;acc:p11310]	Subtracted	206.102	210.42	4.318	
1412	polyposis locus protein 1 (tb2 protein). [source:swissprot;acc:q00765]	Divided	206.102	210.42	1.02095	

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/