MK5 Microarray Data

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 5808 to 5857 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	Network Comparison Type	red	green	network_comparison
726	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	Ranked	Subtracted	222.825	211.966	10.859
727	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	Measured	Divided	7087.23	7911.25	1.11627
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Squared	Subtracted	28801.7	33039.9	4238.2
	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	Rooted		50.268	45.8663	4.4017
	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	Ranked	Divided	208.873	219.71	1.05188
			Subtracted			10.837
	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Rooted	Divided	59.7414	63.909	1.06976
	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348]	Measured	Subtracted	5874.74	6533.33	658.59
	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12]	Squared	Divided	25911.5	30281.9	1.16867
728	60s ribosomal protein l9. [swissprot;acc:p32969]	Rooted	Subtracted	51.1334	46.7335	4.3999
	hcv ns3-transactivated protein 1. [refseq;acc:nm_019048]	Measured	Divided	6000.23	6696.89	1.11611
	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]	Squared	Subtracted	28801.2	33038.7	4237.5
	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]	Ranked	Divided	208.874	219.708	1.05187
			Subtracted			10.834
	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	Rooted	Divided	59.7414	63.909	1.06976
	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281]	Squared		25911.8	30282.2	1.16866
	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543]	Measured	Subtracted	5874.77	6533.36	658.59
729	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Squared		28801.2	33038.6	4237.4
	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	Rooted		50.162	45.7659	4.3961
	exocyst complex component sec15a. [swissprot;acc:q8tag9]		Divided	62.5069	66.8603	1.06965
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Ranked		208.874	219.708	1.05187
			Subtracted			10.834
	vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606]	Measured	Divided	6000.23	6696.89	1.11611
	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313]	Squared		25910.8	30280.9	1.16866
	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12]	Measured	Subtracted	5874.74	6533.33	658.59
730	asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]		Divided	6000.23	6696.89	1.11611
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Squared		24644.9	28800.7	1.16863
	exocyst complex component sec15b. [swissprot;acc:q9y2d4]	Rooted		62.5729	66.9286	1.06961
	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Squared	Subtracted	28800.8	33037.5	4236.7
	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]	Ranked	Divided	208.874	219.708	1.05187
			Subtracted			10.834
	preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	Measured		6276.97	6934.8	657.83
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Rooted		50.6156	46.2239	4.3917
731	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
	6-phosphogluconate dehydrogenase, decarboxylating (ec 1.1.1.44). [swissprot;acc:p52209]	Squared		27031.3	31257.4	4226.1
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Rooted	Divided	98.2298	91.8648	1.06929
	dnaj homolog subfamily b member 11 precursor (er-associated dnaj protein 3) (erj3) (er-associated hsp40 co-chaperone) (hdj9) (pwp1- interacting protein 4). [swissprot;acc:q9ubs4]	Measured	Subtracted	6276.97	6934.8	657.83
	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]	Ranked	Divided	208.874	219.708	1.05187
			Subtracted			10.834
	methyltransferase like 2. [refseq;acc:nm_018396]	Measured	Divided	13241.4	11864	1.1161
	vinculin (metavinculin). [swissprot;acc:p18206]	Squared		27463	32090.3	1.16849
732	40s ribosomal protein s3. [swissprot;acc:p23396]	Rooted	Subtracted	50.6274	46.236	4.3914
	cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]	Measured	Divided	13241.4	11864	1.1161
	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Squared	Subtracted	16424.1	20645.8	4221.7
	polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	Rooted	Divided	51.8444	48.4963	1.06904
	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	Ranked		124.434	118.318	1.05169
	translin. [swissprot;acc:q15631]		Subtracted	224.385	235.131	10.746
	vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487]	Measured		5890.49	6547.9	657.41
		Squared	Divided	26029.8	30414.4	1.16845
733	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	Rooted	Subtracted	50.2954	45.9216	4.3738

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.