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	Network Comparison Type	Value Type	Interaction Map	Filtered	green	red	network_comparison

Results: HTML CSV LaTeX

Showing element 1930 to 1979 of 6456 in total

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

Rank	description	Network Comparison Type	green	red	network_comparison
965	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]	Subtracted	171.42	178.514	7.094
966	tubby protein homolog. [swissprot;acc:p50607]	Divided	204.964	211.987	1.03426
	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	Subtracted	204.732	211.812	7.08
967	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]		238.356	231.277	7.079
	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]	Divided	204.964	211.987	1.03426
968	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Subtracted	125.389	132.413	7.024
	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	Divided	204.964	211.987	1.03426
969	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Subtracted	125.389	132.413	7.024
	tbc1 domain family member 5. [swissprot;acc:q92609]	Divided	204.964	211.987	1.03426
970	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Subtracted	125.389	132.413	7.024
	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	Divided	204.964	211.987	1.03426
971	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Subtracted	125.389	132.413	7.024
	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]	Divided	204.964	211.987	1.03426
972	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Subtracted	125.389	132.413	7.024
	numb-like protein (numb-r). [swissprot;acc:q9y6r0]	Divided	204.964	211.987	1.03426
973	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Subtracted	125.389	132.413	7.024
	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]	Divided	204.964	211.987	1.03426
974	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Subtracted	125.389	132.413	7.024
	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]	Divided	204.964	211.987	1.03426
975	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Subtracted	125.389	132.413	7.024
	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]	Divided	204.964	211.987	1.03426
976	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Subtracted	125.389	132.413	7.024
	t-cell activation wd repeat protein. [refseq;acc:nm_139281]	Divided	235.322	243.34	1.03407
977	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4]	Subtracted	204.964	211.987	7.023
	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	Divided	221.421	228.953	1.03402
978	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
	tubby protein homolog. [swissprot;acc:p50607]	Subtracted	204.964	211.987	7.023
979	gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537]	Divided	195.386	202.027	1.03399
	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743]	Subtracted	204.964	211.987	7.023
980	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	Divided	134.713	130.289	1.03396
	numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]	Subtracted	204.964	211.987	7.023
981	exocyst complex component sec6. [swissprot;acc:o60645]	Divided	200.398	207.186	1.03387
	tbc1 domain family member 5. [swissprot;acc:q92609]	Subtracted	204.964	211.987	7.023
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	Divided	235.351	243.312	1.03383
	tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294]	Subtracted	204.964	211.987	7.023
983	pbk1 protein. [sptrembl;acc:o76021]	Divided	235.353	243.312	1.03382
	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0]	Subtracted	204.964	211.987	7.023
984	numb-like protein (numb-r). [swissprot;acc:q9y6r0]
	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003]	Divided	120.654	116.71	1.03379
985	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]		225.782	233.402	1.03375
	tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386]	Subtracted	204.964	211.987	7.023
986	exocyst complex component sec5. [swissprot;acc:q96kp1]	Divided	120.707	116.771	1.03371
	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1]	Subtracted	204.964	211.987	7.023
987	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
	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]	Divided	211.338	218.459	1.03369
988	probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]		211.343	218.461	1.03368
	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	Subtracted	243.679	236.679	7
989	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	Divided	211.345	218.462	1.03367
	zinc finger protein 277. [swissprot;acc:q9nrm2]	Subtracted	243.679	236.679	7
990	atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	Divided	235.373	243.297	1.03367

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.