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.

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

Results: HTML CSV LaTeX

Showing element 925 to 974 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
463	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	Divided	3720.18	4264.46	1.1463
	f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315]	Subtracted	2353.63	3225.65	872.02
464	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Divided	4858.96	5568.85	1.1461
465	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	Subtracted	2353.63	3225.65	872.02
	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	Divided	3847.31	4409.22	1.14605
466	cullin homolog 1 (cul-1). [swissprot;acc:q13616]	Subtracted	2353.63	3225.65	872.02
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Divided	3847.31	4409.22	1.14605
467	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	Subtracted	1926.69	1056.02	870.67
	metastasis-associated protein mta1. [swissprot;acc:q13330]	Divided	4864.25	5573.62	1.14583
468	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]		4869.15	5578.02	1.14558
	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]	Subtracted	11143.5	10276.3	867.2
469	proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087]	Divided	3831.17	4388.74	1.14554
	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357]	Subtracted	11143.5	10276.3	867.2
470	block of proliferation 1. [swissprot;acc:q14137]	Divided	3796.24	4348.59	1.1455
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Subtracted	5367.04	6233.12	866.08
471	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778]	Divided	9649.61	11053.5	1.14549
	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	Subtracted	5980.15	6843.48	863.33
472	multisynthetase complex auxiliary component p43 [contains: endothelial-monocyte activating polypeptide ii (emap-ii) (small inducible cytokine subfamily e member 1)]. [swissprot;acc:q12904]		5246.01	6109.31	863.3
	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [swissprot;acc:q9nya1]	Divided	9649.61	11053.5	1.14549
473	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]	Subtracted	5979.95	6842.78	862.83
	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	Divided	9649.61	11053.5	1.14549
474	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	Subtracted	5979.94	6842.76	862.82
	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	Divided	9649.61	11053.5	1.14549
475	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	Subtracted	5979.93	6842.72	862.79
	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	Divided	9649.61	11053.5	1.14549
476	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]
	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	Subtracted	5067.02	5926.46	859.44
477	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	Divided	9649.61	11053.5	1.14549
	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	Subtracted	5067	5926.17	859.17
478	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]		5066.99	5926.1	859.11
	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	Divided	9649.61	11053.5	1.14549
479	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	Subtracted	7170.83	8029.64	858.81
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	Divided	9649.61	11053.5	1.14549
480	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]
	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	Subtracted	5066.93	5925.38	858.45
481	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]		5493.1	6350.19	857.09
	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	Divided	9649.61	11053.5	1.14549
482	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]	Subtracted	5493.1	6350.19	857.09
	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [swissprot;acc:q16539]	Divided	9649.61	11053.5	1.14549
483	40s ribosomal protein s28. [swissprot;acc:p25112]	Subtracted	7161.14	8015.92	854.78
	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Divided	9649.61	11053.5	1.14549
484	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Subtracted	7139.5	7994.06	854.56
485	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520]		1881.02	1027.36	853.66
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Divided	9649.61	11053.5	1.14549
486	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	Subtracted	5975.11	6826.24	851.13
	stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975]	Divided	10908.6	12491.8	1.14513
487	pyrroline 5-carboxylate reductase isoform. [refseq;acc:nm_013328]		5277.4	6042.88	1.14505
	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]	Subtracted	5975.11	6826.24	851.13

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.