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.


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 4208 to 4257 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
526 septin 6. [swissprot;acc:q14141] Rooted Divided 113.169 123.23 1.0889
527 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Squared Subtracted 31100.1 36086.4 4986.3
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Ranked Divided 248.56 232.579 1.06871
deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 166.771 1.08865
histone h2b.s (h2b/s). [swissprot;acc:p57053] Ranked Subtracted 247.47 233.441 14.029
protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Measured Divided 4775.11 5438.18 1.13886
Rooted Subtracted 56.3798 61.4858 5.106
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Measured 4700.42 5492.63 792.21
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Squared Divided 18011.9 21552.8 1.19659
528 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] Measured 10635.3 12111.4 1.13879
histone h2b.d (h2b/d). [swissprot;acc:q99877] Ranked Subtracted 247.47 233.441 14.029
mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439] Measured 5244.71 6036.27 791.56
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] Rooted 55.1759 60.2621 5.0862
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Squared 31100.1 36086.4 4986.3
serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Divided 10606 8868.81 1.19588
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Rooted 66.941 72.7546 1.08685
yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Ranked 222.146 237.393 1.06864
529 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] 251.653 235.506 1.06856
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] Rooted Subtracted 55.1759 60.2621 5.0862
histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695] Ranked 247.47 233.441 14.029
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] Squared 31100.1 36086.4 4986.3
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Measured Divided 8600.02 9792.49 1.13866
mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713] Subtracted 5244.88 6036.38 791.5
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Rooted Divided 50.3239 54.6658 1.08628
sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289] Squared 28990.9 34656.4 1.19542
530 40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366] Rooted 50.6537 46.6413 1.08603
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073] Subtracted 55.1759 60.2621 5.0862
monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283] Squared Divided 27179.5 32490.8 1.19542
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Measured 8600.02 9792.49 1.13866
star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4] Squared Subtracted 31100.1 36086.4 4986.3
testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610] Ranked 247.47 233.441 14.029
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Divided 227.483 212.994 1.06803
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Measured Subtracted 5246.38 6037.37 790.99
531 40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232] Rooted Divided 50.6537 46.6413 1.08603
histone h2b.e (h2b/e). [swissprot;acc:q99879] Ranked Subtracted 247.47 233.441 14.029
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Divided 223.356 209.149 1.06793
pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] Rooted Subtracted 55.1759 60.2621 5.0862
prohibitin. [swissprot;acc:p35232] Measured 5773.45 6563.69 790.24
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] Squared 31100.1 36086.4 4986.3
solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913] Divided 28980.7 34643.6 1.1954
transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403] Measured 4651.88 5296.78 1.13863
532 60s ribosomal protein l8. [swissprot;acc:p25120] Rooted Subtracted 55.1759 60.2621 5.0862
kidney and liver proline oxidase 1. [refseq;acc:nm_021232] Squared Divided 28967 34626.4 1.19537
myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] Ranked Subtracted 112 126 14
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283] Squared 31100.1 36086.4 4986.3
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] Measured 5773.45 6563.69 790.24
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Rooted Divided 107.961 117.197 1.08555
thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649] Measured 4651.88 5296.78 1.13863
zinc finger-like protein 9. [refseq;acc:nm_033414] Ranked 250.942 235.004 1.06782
533 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Subtracted 58 44 14

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.
- http://analysis.yellowcouch.org/