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

Results: HTML CSV LaTeX

Showing element 9536 to 9585 of 9634 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : Low confidence
Filtered  : 1

Rank	description	red	green	network_comparison
4963	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	7552.15	7575.73	1.00312
4964	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]	8025.99	8050.95	1.00311
4965	testis-specific bromodomain protein. [refseq;acc:nm_001726]	8801.27	8827.24	1.00295
4966	spermidine synthase (ec 2.5.1.16) (putrescine aminopropyltransferase) (spdsy). [swissprot;acc:p19623]	8921.4	8947.73
4967	sh3-domain binding protein 1 (3bp-1). [swissprot;acc:q9y3l3]	7904.34	7927.66
4968	flavin reductase (ec 1.5.1.30) (fr) (nadph-dependent diaphorase) (nadph-flavin reductase) (flr) (biliverdin reductase b) (ec 1.3.1.24) (bvr-b) (biliverdin-ix beta-reductase) (green heme binding protein) (ghbp). [swissprot;acc:p30043]	7462.96	7441.29	1.00291
4969	protein c6orf55 (dopamine responsive protein drg-1) (my012 protein) (hspc228). [swissprot;acc:q9np79]
4970	solute carrier family 35, member e1. [refseq;acc:nm_024881]	7244.61	7265.04	1.00282
4971	exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027]	8798.12	8773.44	1.00281
4972	28s ribosomal protein s18b, mitochondrial precursor (mrp-s18-b) (mrps18b) (mrp-s18-2) (ptd017 protein) (hspc183). [swissprot;acc:q9y676]	7611.44	7632.4	1.00275
4973	poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3]	8596.74	8620.11	1.00272
4974	5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0]	8903.9	8928.03	1.00271
4975	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	8529.69	8552.73	1.0027
4976	bromodomain-containing protein 2 (ring3 protein) (o27.1.1). [swissprot;acc:p25440]	8815.07	8837.23	1.00251
4977	solute carrier family 35, member e2. [refseq;acc:nm_182838]	7238.71	7256.27	1.00243
4978	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	8606.75	8627.55	1.00242
4979	sodium/potassium-transporting atpase beta-3 chain (sodium/potassium- dependent atpase beta-3 subunit) (atpb-3). [swissprot;acc:p54709]	8648.17	8667.91	1.00228
4980	x/potassium-transporting atpase beta-m chain (x,k-atpase beta-m subunit). [swissprot;acc:q9un42]	8648.53	8668.14	1.00227
4981	serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955]	7681.66	7698.93	1.00225
4982	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	7619.32	7636.37	1.00224
4983	sodium/potassium-transporting atpase beta-2 chain (sodium/potassium- dependent atpase beta-2 subunit). [swissprot;acc:p14415]	8650.11	8669.12	1.0022
4984	short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4]	7525.15	7509.41	1.0021
4985	fatty acid-binding protein, heart (h-fabp) (muscle fatty acid-binding protein) (m-fabp) (mammary-derived growth inhibitor) (mdgi). [swissprot;acc:p05413]	8494.9	8511.92	1.002
4986	ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6]	7527.87	7514.1	1.00183
4987	short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
4988	sec13-related protein. [swissprot;acc:p55735]	9039.42	9023.33	1.00178
4989	cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	9221.87	9237.37	1.00168
4990	fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090]	8502.36	8516.44	1.00166
4991	myelin p2 protein. [swissprot;acc:p02689]	8502.52	8516.53	1.00165
4992	bromodomain-containing protein 3 (ring3-like protein). [swissprot;acc:q15059]	8843.56	8857.85	1.00162
4993	ribonuclease p protein subunit p20 (ec 3.1.26.5) (rnasep protein p20) (hpop7). [swissprot;acc:o75817]	6922.79	6911.72	1.0016
4994	3'(2'), 5'-bisphosphate nucleotidase 1; bisphosphate 3'-nucleotidase; bpntase; pap-inositol-1,4-phosphatase. [refseq;acc:nm_006085]
4995	60s ribosomal protein l6 (tax-responsive enhancer element binding protein 107) (taxreb107) (neoplasm-related protein c140). [swissprot;acc:q02878]
4996	phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [swissprot;acc:q16816]	6636.46	6626.87	1.00145
4997	ring1 and yy1 binding protein; ring1 interactor rybp; yy1 and e4tf1 associated factor 1; apoptin-associating protein 1. [refseq;acc:nm_012234]	7642.51	7653.25	1.00141
4998	yy1 associated factor 2. [refseq;acc:nm_005748]
4999	sodium/potassium-transporting atpase beta-1 chain (sodium/potassium- dependent atpase beta-1 subunit). [swissprot;acc:p05026]	8669.7	8681.33	1.00134
5000	solute carrier family 2, facilitated glucose transporter, member 6 (glucose transporter type 6) (glucose transporter type 9). [swissprot;acc:q9ugq3]	8501.53	8512.12	1.00125
5001	solute carrier family 2, facilitated glucose transporter, member 8 (glucose transporter type 8) (glucose transporter type x1). [swissprot;acc:q9ny64]
5002	programmed cell death 4 isoform 1; programmed cell death 4; nuclear antigen h731. [refseq;acc:nm_014456]	8484.33	8494.43	1.00119
5003	phosphoacetylglucosamine mutase (ec 5.4.2.3) (pagm) (acetylglucosamine phosphomutase) (n-acetylglucosamine-phosphate mutase) (phosphoglucomutase 3). [swissprot;acc:o95394]	8929.2	8939.73	1.00118
5004	ribonuclease p protein subunit p30 (ec 3.1.26.5) (rnasep protein p30) (rnase p subunit 2). [swissprot;acc:p78346]	7255.42	7261.97	1.0009
5005	spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [refseq;acc:nm_005470]	8606.11	8613.6	1.00087
5006	phosphorylase b kinase gamma catalytic chain, testis/liver isoform (ec 2.7.1.38) (phk-gamma-t) (phosphorylase kinase gamma subunit 2) (psk-c3). [swissprot;acc:p15735]	6658.39	6653.12	1.00079
5007	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	9134.61	9127.55	1.00077
5008	abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759]	8608.57	8615.12	1.00076
5009	rab9 effector p40. [refseq;acc:nm_005833]	8545.09	8538.63
5010	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	9142.82	9136.28	1.00072
5011	exocyst complex component exo70. [swissprot;acc:q9upt5]	7172.29	7168.41	1.00054
5012	rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756]	9412.17	9416.13	1.00042

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.