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 768 to 817 of 3730 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	green	network_comparison
384	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	0	8243.06	8627.63	1.04665
385	40s ribosomal protein s28. [swissprot;acc:p25112]		387.486	405.367	1.04615
	pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222]	1	4533.74	5279.4	1.16447
386	60s ribosomal protein l8. [swissprot;acc:p25120]
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	0	2156.64	2254.12	1.0452
387	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]		1388.29	1330.37	1.04354
	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	1	4533.74	5279.4	1.16447
388	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]
	scratch; scratch 1. [refseq;acc:nm_031309]	0	1398.21	1339.9	1.04352
389	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]		11512.3	12011.7	1.04338
	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	1	4533.74	5279.4	1.16447
390	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	0	11512.3	12011.7	1.04338
	rw1 protein (fragment). [swissprot;acc:q92545]	1	4533.74	5279.4	1.16447
391	seven in absentia homolog 1. [refseq;acc:nm_003031]	0	2221.04	2316.94	1.04318
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	1	3658.76	3144.39	1.16358
392	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	0	229.211	219.891	1.04238
	atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	1	3641.89	4236.95	1.16339
393	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]		4490.28	5222.25	1.16301
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	0	2131.42	2218.51	1.04086
394	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	1	4490.28	5222.25	1.16301
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	0	2131.52	2218.58	1.04084
395	histone h2b.s (h2b/s). [swissprot;acc:p57053]		2131.83	2218.82	1.04081
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	1	4532.73	5269.33	1.16251
396	histone h2b. [refseq;acc:nm_175055]	0	2131.91	2218.89	1.0408
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	1	6563.65	7627.29	1.16205
397	histone h2b.e (h2b/e). [swissprot;acc:q99879]	0	2131.93	2218.9	1.04079
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	1	5367.04	6233.12	1.16137
398	histone h2b.c (h2b/c). [swissprot;acc:q99880]	0	2132.04	2218.98	1.04078
	xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7]	1	5084.26	5904.1	1.16125
399	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]	0	548.5	527.5	1.03981
	neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544]	1	5201.41	4479.76	1.16109
400	adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
	myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623]	0	548.5	527.5	1.03981
401	adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622]	1	5201.41	4479.76	1.16109
	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	0	548.5	527.5	1.03981
402	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	1	5201.41	4479.76	1.16109
	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	0	548.5	527.5	1.03981
403	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	1	5201.41	4479.76	1.16109
	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	0	548.5	527.5	1.03981
404	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	1	5201.41	4479.76	1.16109
	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	0	1229.57	1278.36	1.03968
405	integral membrane protein cii-3b. [sptrembl;acc:o75609]		2218.63	2304.22	1.03858
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	1	5201.41	4479.76	1.16109
406	thymic stromal co-transporter. [refseq;acc:nm_033051]
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	0	2363.32	2454.04	1.03839
407	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]		3614.24	3481.87	1.03802
	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	1	6603.41	7664.65	1.16071
408	dok-like protein. [refseq;acc:nm_024872]		6102.59	7081.46	1.1604
	glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409]	0	219.031	227.143	1.03704
409	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	1	6102.59	7081.46	1.1604

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.