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 2808 to 2857 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
176	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33]	Ranked	Divided	1	275.754	235.908	1.1689
	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]		Subtracted		271.016	244.167	26.849
	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	Measured			10235.2	11830.8	1595.6
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Squared		0	3680.47	3222.63	457.84
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Rooted			23.871	20.9159	2.9551
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Measured	Divided	1	4456.93	5773.67	1.29544
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	Rooted			145.551	168.796	1.1597
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Squared	Subtracted		71576.8	56326.7	15250.1
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Measured	Divided	0	3023.85	2436.4	1.24111
177	acrc protein; putative nuclear protein. [refseq;acc:nm_052957]				4131.06	3340.03	1.23683
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Squared	Subtracted	1	9924.76	25146.6	15221.8
	dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2]	Ranked	Divided		229.406	196.695	1.1663
	dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325]	Rooted		0	20.3458	17.7104	1.14881
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Squared			73.1683	109.766	1.50019
	keratin associated protein 1.5. [refseq;acc:nm_031957]		Subtracted		3680.43	3222.6	457.83
	lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075]	Measured		1	4110.14	5694.99	1584.85
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]		Divided		4457.06	5773.63	1.29539
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	Rooted			145.551	168.796	1.1597
	mstp028 protein. [refseq;acc:nm_031954]		Subtracted	0	64.9832	62.0398	2.9434
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	Measured			1124.15	943.423	180.727
	pnas-18. [sptrembl;acc:q9bzu3]	Ranked			12602.7	13939.6	1336.9
	potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]		Divided		14922.7	13174.5	1.1327
	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Rooted	Subtracted	1	37.3005	48.4141	11.1136
	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	Squared	Divided		78383	108483	1.38401
	transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477]	Ranked	Subtracted		241.07	267.88	26.81
178	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	Squared			9924.76	25146.6	15221.8
	carboxypeptidase b precursor. [refseq;acc:nm_020361]		Divided		25326.4	18354.1	1.37988
	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Rooted		0	35.0775	30.5361	1.14872
	cullin homolog 1 (cul-1). [swissprot;acc:q13616]		Subtracted	1	37.3005	48.4141	11.1136
	dc11 protein. [refseq;acc:nm_020186]	Squared	Divided	0	73.1683	109.766	1.50019
	density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]	Ranked	Subtracted	1	241.07	267.88	26.81
	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	Measured	Divided	0	498.07	615.233	1.23523
	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	Ranked		1	226.887	194.72	1.1652
	integral membrane protein cii-3b. [sptrembl;acc:o75609]			0	14951.6	13204.2	1.13234
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]	Squared	Subtracted		3680.43	3222.6	457.83
	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	Rooted			12.6886	9.74679	2.94181
	mstp028 protein. [refseq;acc:nm_031954]	Measured			9988.45	9808.48	179.97
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]		Divided	1	21591.5	27904.5	1.29238
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]		Subtracted		10908.6	12491.8	1583.2
	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	Rooted	Divided		45.7414	52.932	1.1572
	transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	Ranked	Subtracted	0	10899.5	12217.4	1317.9
179	20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298]	Measured		1	4266.04	5843.51	1577.47
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Ranked		0	12190.3	13497.2	1306.9
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Measured	Divided		556	681	1.22482
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Rooted	Subtracted	1	55.0737	66.0298	10.9561
	huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404]	Ranked	Divided		226.884	194.79	1.16476
	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Rooted	Subtracted	0	23.8722	20.933	2.9392
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Squared			3680.39	3222.57	457.82
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]		Divided	1	25326.3	18354.1	1.37987
	mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426]	Ranked		0	9473.01	10723.7	1.13203

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.