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 1901 to 1950 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
951 dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122] Low confidence 203.779 198.841 1.02483
triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962] High confidence 217.253 209.827 1.03539
952 target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678] 217.252 209.83 1.03537
vacuolar proton translocating atpase 116 kda subunit a isoform 2 (v-atpase 116-kda isoform a2) (tj6). [swissprot;acc:q9y487] Low confidence 190.738 186.118 1.02482
953 heat shock factor binding protein 1. [swissprot;acc:o75506] 206.826 201.818 1.02481
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] High confidence 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
vacuolar proton translocating atpase 116 kda subunit a isoform 3 (v- atpase 116-kda isoform a3) (osteoclastic proton pump 116 kda subunit) (oc-116 kda) (oc116) (t-cell immune regulator 1) (t cell immune response cdna7 protein) (tirc7). [swissprot;acc:q13488] Low confidence 190.801 186.183 1.0248
955 mitochondrial 60s ribosomal protein l27 (l27mt) (hspc250). [swissprot;acc:q9p0m9] High confidence 231.163 239.205 1.03479
neural wiskott-aldrich syndrome protein (n-wasp). [swissprot;acc:o00401] Low confidence 198.172 193.377 1.0248
956 putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] 203.365 198.452 1.02476
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] High confidence 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
transcription initiation factor tfiid 70 kda subunit (tafii-70) (tafii-80) (tafii80). [swissprot;acc:p49848] Low confidence 201.82 196.944 1.02476
958 probable serine/threonine protein kinase snf1lk (ec 2.7.1.-). [swissprot;acc:p57059] 194.842 190.136 1.02475
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049] High confidence 129.921 134.406 1.03452
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] 237.558 229.677 1.03431
single-stranded dna-binding protein, mitochondrial precursor (mt-ssb) (mtssb) (pwp1-interacting protein 17). [swissprot;acc:q04837] Low confidence 194.842 190.136 1.02475
960 sodium/iodide cotransporter (na(+)/i(-) cotransporter) (sodium-iodide symporter) (na+/i-symporter). [swissprot;acc:q92911] 200.05 195.223 1.02473
zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] High confidence 237.558 229.677 1.03431
961 phosphatidylinositol-binding clathrin assembly protein (clathrin assembly lymphoid myeloid leukemia protein). [swissprot;acc:q13492] Low confidence 203.548 198.638 1.02472
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] High confidence 130.066 134.527 1.0343
962 cyclin g2. [swissprot;acc:q16589]
polymerase (dna directed), eta. [refseq;acc:nm_006502] Low confidence 201.09 196.241 1.02471
963 cyclin g1 (cyclin g). [swissprot;acc:p51959] High confidence 130.066 134.527 1.0343
integral membrane protein 2b (transmembrane protein bri) [contains: abri/adan amyloid peptide]. [swissprot;acc:q9y287] Low confidence 201.992 197.121 1.02471
964 integral membrane protein 2c (transmembrane protein bri3) (npd018). [swissprot;acc:q9nqx7]
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] High confidence 130.066 134.527 1.0343
965 integral membrane protein 2a (e25 protein). [swissprot;acc:o43736] Low confidence 201.992 197.121 1.02471
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] High confidence 211.987 204.964 1.03426
966 proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80] Low confidence 206.197 201.227 1.0247
tubby protein homolog. [swissprot;acc:p50607] High confidence 211.987 204.964 1.03426
967 lysine-deficient protein kinase 2; mitogen-activated protein kinase kinase kinase; serologically defined colon cancer antigen 43. [refseq;acc:nm_006648] Low confidence 204.782 199.848 1.02469
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] High confidence 211.987 204.964 1.03426
968 numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757]
protein kinase, lysine deficient 4; putative protein kinase wnk4. [refseq;acc:nm_032387] Low confidence 204.782 199.848 1.02469
969 protein kinase, lysine deficient 3. [refseq;acc:nm_020922]
tbc1 domain family member 5. [swissprot;acc:q92609] High confidence 211.987 204.964 1.03426
970 protein kinase, lysine deficient 1; kinase deficient protein. [refseq;acc:nm_018979] Low confidence 204.782 199.848 1.02469
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] High confidence 211.987 204.964 1.03426
971 exonuclease nef-sp. [refseq;acc:nm_030941] Low confidence 204.782 199.848 1.02469
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] High confidence 211.987 204.964 1.03426
972 atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859] Low confidence 202.474 197.597 1.02468
numb-like protein (numb-r). [swissprot;acc:q9y6r0] High confidence 211.987 204.964 1.03426
973 centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264] Low confidence 202.474 197.597 1.02468
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] High confidence 211.987 204.964 1.03426
974 nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991] Low confidence 204.273 199.353 1.02468
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] High confidence 211.987 204.964 1.03426
975 protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513]
translation initiation factor if-2. [swissprot;acc:o60841] Low confidence 202.576 197.699 1.02467

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/