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 Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1900 to 1949 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
950 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Subtracted 225.167 217.922 7.245
951 sprouty homolog 2 (spry-2). [swissprot;acc:o43597]
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] Divided 217.253 209.827 1.03539
952 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Subtracted 225.448 218.232 7.216
target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] Divided 217.252 209.83 1.03537
953 c-type lectin superfamily member 1 precursor (cartilage-derived c-type lectin). [swissprot;acc:o75596] Subtracted 178.033 170.82 7.213
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Divided 198.494 205.466 1.03512
954 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 267.447 276.773 1.03487
thioredoxin-like; pkc-interacting cousin of thioredoxin. [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. [refseq;acc:nm_004742] 221.73 228.906 7.176
mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] Divided 231.163 239.205 1.03479
956 t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [swissprot;acc:p17987] Subtracted 135.379 128.225 7.154
vinexin (sh3-containing adaptor molecule-1) (scam-1). [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). [swissprot;acc:p10398] 129.913 134.399 1.03453
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [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). [swissprot;acc:p04049] Divided 129.921 134.406 1.03452
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 218.459 211.338 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). [swissprot;acc:p25388] Divided 237.558 229.677 1.03431
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105] Subtracted 218.461 211.343 7.118
960 probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] 218.462 211.345 7.117
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Divided 237.558 229.677 1.03431
961 serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Subtracted 218.468 211.357 7.111
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 130.066 134.527 1.0343
962 cyclin g2. [swissprot;acc:q16589]
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Subtracted 219.656 212.547 7.109
963 cyclin g1 (cyclin g). [swissprot;acc:p51959] Divided 130.066 134.527 1.0343
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Subtracted 219.656 212.547 7.109
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 130.066 134.527 1.0343
965 partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] 211.987 204.964 1.03426
tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452] Subtracted 178.514 171.42 7.094
966 tubby protein homolog. [swissprot;acc:p50607] Divided 211.987 204.964 1.03426
vinexin (sh3-containing adaptor molecule-1) (scam-1). [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). [swissprot;acc:q9y2s0] 231.277 238.356 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 211.987 204.964 1.03426
968 homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Subtracted 132.413 125.389 7.024
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Divided 211.987 204.964 1.03426
969 homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Subtracted 132.413 125.389 7.024
tbc1 domain family member 5. [swissprot;acc:q92609] Divided 211.987 204.964 1.03426
970 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Subtracted 132.413 125.389 7.024
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Divided 211.987 204.964 1.03426
971 homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 132.413 125.389 7.024
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Divided 211.987 204.964 1.03426
972 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 132.413 125.389 7.024
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Divided 211.987 204.964 1.03426
973 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 132.413 125.389 7.024
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Divided 211.987 204.964 1.03426
974 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 132.413 125.389 7.024
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Divided 211.987 204.964 1.03426
975 homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted 132.413 125.389 7.024

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/