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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Rank Gene description Network Comparison Type Value Type Interaction Map red network_comparison Filtered green
Results: HTML CSV LaTeX Showing element 1913 to 1962 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
network_comparison
green
957 a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398] Divided 129.913 1.03453 134.399
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6] Subtracted 168.592 7.14 161.452
958 raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] Divided 129.921 1.03452 134.406
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] Subtracted 218.459 7.121 211.338
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). [swissprot;acc:p25388] Divided 237.558 1.03431 229.677
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Subtracted 218.461 7.118 211.343
960 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 218.462 7.117 211.345
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Divided 237.558 1.03431 229.677
961 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Subtracted 218.468 7.111 211.357
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). [swissprot;acc:q16537] Divided 130.066 1.0343 134.527
962 cyclin g2. [swissprot;acc:q16589]
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Subtracted 219.656 7.109 212.547
963 cyclin g1 (cyclin g). [swissprot;acc:p51959] Divided 130.066 1.0343 134.527
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 219.656 7.109 212.547
964 nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
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). [swissprot;acc:q15172] Divided 130.066 1.0343 134.527
965 partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 211.987 1.03426 204.964
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Subtracted 178.514 7.094 171.42
966 tubby protein homolog. [swissprot;acc:p50607] Divided 211.987 1.03426 204.964
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Subtracted 211.812 7.08 204.732
967 dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0] 231.277 7.079 238.356
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 211.987 1.03426 204.964
968 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 132.413 7.024 125.389
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Divided 211.987 1.03426 204.964
969 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Subtracted 132.413 7.024 125.389
tbc1 domain family member 5. [swissprot;acc:q92609] Divided 211.987 1.03426 204.964
970 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted 132.413 7.024 125.389
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Divided 211.987 1.03426 204.964
971 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 132.413 7.024 125.389
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Divided 211.987 1.03426 204.964
972 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 132.413 7.024 125.389
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Divided 211.987 1.03426 204.964
973 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 132.413 7.024 125.389
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Divided 211.987 1.03426 204.964
974 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 132.413 7.024 125.389
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Divided 211.987 1.03426 204.964
975 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 132.413 7.024 125.389
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Divided 211.987 1.03426 204.964
976 retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Subtracted 132.413 7.024 125.389
t-cell activation wd repeat protein. [refseq;acc:nm_139281] Divided 243.34 1.03407 235.322
977 partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Subtracted 211.987 7.023 204.964
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471] Divided 228.953 1.03402 221.421
978 prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
tubby protein homolog. [swissprot;acc:p50607] Subtracted 211.987 7.023 204.964
979 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Divided 202.027 1.03399 195.386
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 211.987 7.023 204.964
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 130.289 1.03396 134.713
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Subtracted 211.987 7.023 204.964
981 exocyst complex component sec6. [swissprot;acc:o60645] Divided 207.186 1.03387 200.398
tbc1 domain family member 5. [swissprot;acc:q92609] Subtracted 211.987 7.023 204.964

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/