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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 977 to 1026 of 3228 in total

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

red	green	Rank	description	network_comparison
4640.26	5704.87	242	max protein. [swissprot;acc:p25912]	1.22943
4641.09	5588.75	292	nucleotide-binding protein 1 (nbp 1). [swissprot;acc:p53384]	1.20419
		293	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]
4644.04	4470.47	2412	dynactin 4. [refseq;acc:nm_032486]	1.03883
4644.58	4892.06	2148	deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321]	1.05328
4651.88	5296.78	531	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403]	1.13863
		532	thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]
		533	nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769]
		534	nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345]
4668.29	4868.52	2371	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]	1.04289
4673.96	4876.71	2362	dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959]	1.04338
4674.38	4877.31	2361	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]	1.04341
4682.87	4093.05	496	nostrin. [refseq;acc:nm_052946]	1.1441
		497	eap30 subunit of ell complex. [refseq;acc:nm_007241]
		498	liv-1 protein, estrogen regulated. [refseq;acc:nm_012319]
		499	glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
		500	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]
		501	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]
4682.88	5646.19	289	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	1.20571
4689.78	4973.44	1956	nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062]	1.06048
4700.42	5492.63	375	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116]	1.16854
4708.61	5226.71	805	60s ribosomal protein l39. [swissprot;acc:p02404]	1.11003
		806	60s ribosomal protein l18a. [swissprot;acc:q02543]
		807	40s ribosomal protein s19. [swissprot;acc:p39019]
		808	60s ribosomal protein l31. [swissprot;acc:p12947]
4708.68	4702.58	2747	putatative 28 kda protein. [refseq;acc:nm_020143]	1.0013
4708.98	4817.39	2542	osteoclast stimulating factor 1. [swissprot;acc:q92882]	1.02302
4713.58	4279.17	900	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	1.10152
4714.85	5554.38	349	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	1.17806
4723.53	5828.46	236	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	1.23392
4725.28	5261.06	756	topoisomerase-related function protein 4-2. [refseq;acc:nm_022447]	1.11339
4725.79	4824.4	2548	60s ribosomal protein l37 (g1.16). [swissprot;acc:p02403]	1.02087
		2549	splicing factor, arginine/serine-rich 1 (pre-mrna splicing factor sf2, p33 subunit) (alternative splicing factor asf-1). [swissprot;acc:q07955]
		2550	amidophosphoribosyltransferase precursor (ec 2.4.2.14) (glutamine phosphoribosylpyrophosphate amidotransferase) (atase) (gpat). [swissprot;acc:q06203]
		2551	sorting nexin 17. [swissprot;acc:q15036]
4726.38	5258.95	765	polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999]	1.11268
4730.66	4891.26	2440	u3 snornp protein 4 homolog. [refseq;acc:nm_033416]	1.03395
4749.52	5237.77	873	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	1.1028
4751.74	4900.37	2458	presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	1.03128
		2459	gtp-binding nuclear protein ran (tc4) (ran gtpase) (androgen receptor- associated protein 24). [swissprot;acc:p17080]
		2460	presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]
4757.46	5198.91	1044	mbd2 (methyl-cpg-binding protein)-interacting zinc finger protein. [refseq;acc:nm_015517]	1.09279
		1046	skeletal muscle tropomodulin (sk-tmod) (tropomodulin 4). [swissprot;acc:q9nzq9]
		1047	ubiquitous tropomodulin (u-tmod) (tropomodulin 3). [swissprot;acc:q9nyl9]
		1048	tropomodulin 1 (erythrocyte tropomodulin) (e-tmod). [swissprot;acc:p28289]
		1049	sorting nexin 9 (sh3 and px domain-containing protein 1) (sdp1 protein). [swissprot;acc:q9y5x1]
		1050	neuronal tropomodulin (n-tmod) (tropomodulin 2). [swissprot;acc:q9nzr1]
		1051	homeobox protein dlx-2. [swissprot;acc:q07687]
		1052	homeobox protein dlx-5. [swissprot;acc:p56178]
		1053	fetal brain protein 239 (239fb). [swissprot;acc:q15777]

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.