Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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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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 red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1927 to 1976 of 6456 in total 
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

Rank	description	Network Comparison Type	red	green	network_comparison	
964	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	Subtracted	219.656	212.547	7.109	
964	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [source:swissprot;acc:q15172]	Divided	130.066	134.527	1.0343	
965	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	Divided	211.987	204.964	1.03426	
965	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [source:swissprot;acc:p05452]	Subtracted	178.514	171.42	7.094	
966	tubby protein homolog. [source:swissprot;acc:p50607]	Divided	211.987	204.964	1.03426	
966	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	Subtracted	211.812	204.732	7.08	
967	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [source:swissprot;acc:q9y2s0]	Subtracted	231.277	238.356	7.079	
967	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	Divided	211.987	204.964	1.03426	
968	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Subtracted	132.413	125.389	7.024	
968	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	Divided	211.987	204.964	1.03426	
969	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Subtracted	132.413	125.389	7.024	
969	tbc1 domain family member 5. [source:swissprot;acc:q92609]	Divided	211.987	204.964	1.03426	
970	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Subtracted	132.413	125.389	7.024	
970	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	Divided	211.987	204.964	1.03426	
971	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Subtracted	132.413	125.389	7.024	
971	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	Divided	211.987	204.964	1.03426	
972	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Subtracted	132.413	125.389	7.024	
972	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	Divided	211.987	204.964	1.03426	
973	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Subtracted	132.413	125.389	7.024	
973	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	Divided	211.987	204.964	1.03426	
974	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Subtracted	132.413	125.389	7.024	
974	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	Divided	211.987	204.964	1.03426	
975	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Subtracted	132.413	125.389	7.024	
975	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	Divided	211.987	204.964	1.03426	
976	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Subtracted	132.413	125.389	7.024	
976	t-cell activation wd repeat protein. [source:refseq;acc:nm_139281]	Divided	243.34	235.322	1.03407	
977	partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	Subtracted	211.987	204.964	7.023	
977	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [source:swissprot;acc:q99471]	Divided	228.953	221.421	1.03402	
978	prefoldin subunit 6 (protein ke2). [source:swissprot;acc:o15212]	Divided	228.953	221.421	1.03402	
978	tubby protein homolog. [source:swissprot;acc:p50607]	Subtracted	211.987	204.964	7.023	
979	gcn5-like protein 1 (rt14 protein). [source:swissprot;acc:p78537]	Divided	202.027	195.386	1.03399	
979	protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [source:swissprot;acc:p41743]	Subtracted	211.987	204.964	7.023	
980	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [source:swissprot;acc:p15056]	Divided	130.289	134.713	1.03396	
980	numb protein homolog (h-numb) (protein s171). [source:swissprot;acc:p49757]	Subtracted	211.987	204.964	7.023	
981	exocyst complex component sec6. [source:swissprot;acc:o60645]	Divided	207.186	200.398	1.03387	
981	tbc1 domain family member 5. [source:swissprot;acc:q92609]	Subtracted	211.987	204.964	7.023	
982	cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [source:refseq;acc:nm_032830]	Divided	243.312	235.351	1.03383	
982	tubby related protein 1 (tubby-like protein 1). [source:swissprot;acc:o00294]	Subtracted	211.987	204.964	7.023	
983	pbk1 protein. [source:sptrembl;acc:o76021]	Divided	243.312	235.353	1.03382	
983	vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [source:swissprot;acc:q9ubq0]	Subtracted	211.987	204.964	7.023	
984	numb-like protein (numb-r). [source:swissprot;acc:q9y6r0]	Subtracted	211.987	204.964	7.023	
984	poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [source:swissprot;acc:p51003]	Divided	116.71	120.654	1.03379	
985	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [source:swissprot;acc:o14737]	Divided	233.402	225.782	1.03375	
985	tubby related protein 3 (tubby-like protein 3). [source:swissprot;acc:o75386]	Subtracted	211.987	204.964	7.023	
986	exocyst complex component sec5. [source:swissprot;acc:q96kp1]	Divided	116.771	120.707	1.03371	
986	vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [source:swissprot;acc:q96qk1]	Subtracted	211.987	204.964	7.023	
987	protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [source:swissprot;acc:q05513]	Subtracted	211.987	204.964	7.023	
987	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [source:swissprot;acc:o43464]	Divided	218.459	211.338	1.03369	
988	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	Divided	218.461	211.343	1.03368	
988	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Subtracted	236.679	243.679	7	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/