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	Filtered	Network Comparison Type	Interaction Map	green	network_comparison	red

Results: HTML CSV LaTeX

Showing element 610 to 659 of 8289 in total

Value Type  : Ranked
Filtered  : 1
Network Comparison Type  : Divided

Rank	description	Interaction Map	green	network_comparison	red
305	mitochondrial ribosomal protein l2. [refseq;acc:nm_015950]	High confidence	266.986	1.1017	242.339
306	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]		266.673	1.10126	242.153
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Low confidence	193.867	1.04258	202.122
307	phosphorylase b kinase gamma catalytic chain, skeletal muscle isoform (ec 2.7.1.38) (phosphorylase kinase gamma subunit 1). [swissprot;acc:q16816]		227.209	1.04245	217.957
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	High confidence	266.673	1.10126	242.153
308	60s ribosomal protein l34. [swissprot;acc:p49207]
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Low confidence	201.475	1.0424	210.018
309	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]		192.103	1.04222	200.213
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	High confidence	266.673	1.10126	242.153
310	nadh-ubiquinone oxidoreductase 39 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-39kd) (ci-39kd). [swissprot;acc:q16795]	Low confidence	197.484	1.04186	205.75
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	High confidence	266.673	1.10126	242.153
311	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]		267.151	1.10108	242.627
	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]	Low confidence	184.374	1.04184	192.088
312	60s ribosomal protein l3-like. [swissprot;acc:q92901]	High confidence	266.663	1.10103	242.195
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	Low confidence	193.937	1.04184	202.051
313	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		193.94	1.04182	202.05
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	High confidence	211.207	1.10069	232.473
314	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]		268.604	1.10027	244.126
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Low confidence	193.952	1.04179	202.057
315	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	High confidence	268.604	1.10027	244.126
	tankyrase 1 (ec 2.4.2.30) (tank1) (tankyrase i) (tnks-1) (trf1- interacting ankyrin-related adp-ribose polymerase). [swissprot;acc:o95271]	Low confidence	205.509	1.04164	214.067
316	potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]		201.251	1.0414	209.583
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	High confidence	267.017	1.10022	242.694
317	potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	Low confidence	201.251	1.04139	209.58
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	High confidence	204.044	1.09998	224.445
318	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]		266.18	1.09987	242.011
	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	Low confidence	201.251	1.04138	209.579
319	60s ribosomal protein l19. [swissprot;acc:p14118]	High confidence	264.729	1.09969	240.73
	heat-shock protein, beta-2 (hspb2) (dmpk-binding protein) (mkbp). [swissprot;acc:q16082]	Low confidence	204.328	1.04123	212.752
320	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	High confidence	265.96	1.0995	241.892
	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]	Low confidence	226.722	1.04117	217.756
321	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	High confidence	265.959	1.09949	241.892
	glioma tumor suppressor candidate region gene 2 protein (p60). [swissprot;acc:q9nzm5]	Low confidence	199.219	1.04108	207.402
322	cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006]		203.991	1.04055	212.262
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	High confidence	78.8995	1.09948	86.7483
323	60s ribosomal protein l23a. [swissprot;acc:p29316]		265.945	1.09947	241.884
	integrin beta-1 binding protein 2 (melusin) (mstp015). [swissprot;acc:q9ukp3]	Low confidence	203.991	1.04055	212.262
324	40s ribosomal protein s23. [swissprot;acc:p39028]	High confidence	268.195	1.09941	243.944
	rab3 gtpase-activating protein, non-catalytic subunit. [refseq;acc:nm_012414]	Low confidence	203.991	1.04055	212.262
325	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	High confidence	268.195	1.09941	243.944
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Low confidence	192.123	1.04051	199.905
326	60s ribosomal protein l5. [swissprot;acc:p46777]	High confidence	265.924	1.09932	241.899
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Low confidence	191.59	1.04047	199.343
327	bet3 homolog. [swissprot;acc:o43617]		189.574	1.04034	197.221
	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	High confidence	267.962	1.09903	243.817
328	atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]		235.183	1.09888	258.437
	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	Low confidence	195.289	1.04031	203.162
329	exocyst complex component exo70. [swissprot;acc:q9upt5]		212.339	1.04025	204.124
	neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784]	High confidence	284	1.09859	312
330	chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]

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.