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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • 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 [...,...].
    Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
    Results: HTML CSV LaTeX Showing element 1908 to 1957 of 6456 in total 
    Value Type	Ranked
    Interaction Map	High confidence
    Filtered	1
    
Rank	description	Network Comparison Type	red	green	network_comparison	
954	thioredoxin-like; pkc-interacting cousin of thioredoxin. [source:refseq;acc:nm_006541]	Subtracted	228.412	235.609	7.197	
955	bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [source:refseq;acc:nm_004742]	Subtracted	221.73	228.906	7.176	
955	mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [source:swissprot;acc:q9p0m9]	Divided	231.163	239.205	1.03479	
956	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Subtracted	135.379	128.225	7.154	
956	vinexin (sh3-containing adaptor molecule-1) (scam-1). [source:swissprot;acc:o60504]	Divided	211.812	204.732	1.03458	
957	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [source:swissprot;acc:p10398]	Divided	129.913	134.399	1.03453	
957	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [source:swissprot;acc:q9nzl6]	Subtracted	168.592	161.452	7.14	
958	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [source:swissprot;acc:p04049]	Divided	129.921	134.406	1.03452	
958	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]	Subtracted	218.459	211.338	7.121	
959	guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [source:swissprot;acc:p25388]	Divided	237.558	229.677	1.03431	
959	probable serine protease htra4 precursor (ec 3.4.21.-). [source:swissprot;acc:p83105]	Subtracted	218.461	211.343	7.118	
960	probable serine protease htra3 precursor (ec 3.4.21.-). [source:swissprot;acc:p83110]	Subtracted	218.462	211.345	7.117	
960	zuotin related factor-1 (m-phase phosphoprotein 11). [source:swissprot;acc:q99543]	Divided	237.558	229.677	1.03431	
961	serine protease htra1 precursor (ec 3.4.21.-) (l56). [source:swissprot;acc:q92743]	Subtracted	218.468	211.357	7.111	
961	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [source:swissprot;acc:q16537]	Divided	130.066	134.527	1.0343	
962	cyclin g2. [source:swissprot;acc:q16589]	Divided	130.066	134.527	1.0343	
962	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	Subtracted	219.656	212.547	7.109	
963	cyclin g1 (cyclin g). [source:swissprot;acc:p51959]	Divided	130.066	134.527	1.0343	
963	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Subtracted	219.656	212.547	7.109	
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	

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/