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

Results: HTML CSV LaTeX

Showing element 3680 to 3729 of 6456 in total

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

Rank	description	red	green	network_comparison
452	tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	398.5	1281.5	883
453	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]
454	cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627]
455	cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912]
456	ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]
457	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	4620.76	5501.94	881.18
458	grb2-related adaptor protein. [swissprot;acc:q13588]	5986.65	6865.68	879.03
459	pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	5082.66	5959.99	877.33
460	guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901]	1931.34	1057.39	873.95
461	presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	2353.63	3225.65	872.02
462	s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991]
463	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]
464	cullin homolog 2 (cul-2). [swissprot;acc:q13617]
465	presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]
466	cullin homolog 1 (cul-1). [swissprot;acc:q13616]
467	guanine nucleotide-binding protein beta subunit 4 (transducin beta chain 4). [swissprot;acc:q9hav0]	1926.69	1056.02	870.67
468	ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965]	11143.5	10276.3	867.2
469	ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357]
470	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	5367.04	6233.12	866.08
471	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]	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
473	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903]	5979.95	6842.78	862.83
474	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	5979.94	6842.76	862.82
475	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	5979.93	6842.72	862.79
476	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]	5067.02	5926.46	859.44
477	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	5067	5926.17	859.17
478	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	5066.99	5926.1	859.11
479	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304]	7170.83	8029.64	858.81
480	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	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
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]
483	40s ribosomal protein s28. [swissprot;acc:p25112]	7161.14	8015.92	854.78
484	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]	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
486	growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354]	5975.11	6826.24	851.13
487	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]
488	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	7105.27	7953.71	848.44
489	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	7101.95	7949.85	847.9
490	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	7101.94	7949.84
491	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963]	7067.46	7909.27	841.81
492	selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611]	6167.93	7007.7	839.77
493	flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
494	inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866]
495	selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903]
496	inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]
497	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	4714.85	5554.38	839.53
498	transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290]	6933.17	7766.54	833.37
499	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	6938.22	7770.65	832.43
500	huntingtin interacting protein 1 (hip-i). [swissprot;acc:o00291]	10733.4	9902.6	830.8
501	goodpasture antigen-binding protein (ec 2.7.1.37) (gpbp) (collagen type iv alpha 3 binding protein) (star-related lipid transfer protein 11) (stard11) (start domain-containing protein 11). [swissprot;acc:q9y5p4]	10725.6	9896.32	829.28

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.