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 1880 to 1929 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
940 vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Low confidence 202.747 197.81 1.02496
941 2-hydroxyphytanoyl-coa lyase (ec 4.1.-.-) (2-hpcl) (hspc279). [swissprot;acc:q9uj83] 207.026 201.99 1.02493
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] High confidence 212.437 205.083 1.03586
942 grancalcin. [swissprot;acc:p28676] 212.442 205.088
lin-7 homolog c; lin-7 protein 3. [refseq;acc:nm_018362] Low confidence 207.862 202.809 1.02492
943 nadh-ubiquinone oxidoreductase sgdh subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-sgdh) (ci-sgdh). [swissprot;acc:o43674] 205.602 200.603
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] High confidence 212.442 205.087 1.03586
944 growth hormone inducible transmembrane protein (dermal papilla derived protein 2) (my021 protein) (ptd010). [swissprot;acc:q9h3k2] Low confidence 204.752 199.775 1.02491
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] High confidence 212.437 205.083 1.03586
945 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 212.44 205.085
sedlin. [swissprot;acc:o14582] Low confidence 195.693 190.937 1.02491
946 histone h4. [swissprot;acc:p02304] High confidence 227.765 219.902 1.03576
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Low confidence 204.752 199.775 1.02491
947 ad24 protein. [refseq;acc:nm_022451] 203.472 198.533 1.02488
arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069] High confidence 212.51 205.191 1.03567
948 t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Low confidence 209.239 204.165 1.02485
target of myb protein 1. [swissprot;acc:o60784] High confidence 217.254 209.824 1.03541
949 3-oxo-5-alpha-steroid 4-dehydrogenase 1 (ec 1.3.99.5) (steroid 5-alpha-reductase 1) (sr type 1) (s5ar). [swissprot;acc:p18405] Low confidence 204.147 199.196 1.02485
huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229] High confidence 217.253 209.826 1.0354
950 3-oxo-5-alpha-steroid 4-dehydrogenase 2 (ec 1.3.99.5) (steroid 5-alpha-reductase 2) (sr type 2) (5 alpha-sr2). [swissprot;acc:p31213] Low confidence 204.147 199.196 1.02485
dna-repair protein complementing xp-g cells (xeroderma pigmentosum group g complementing protein) (dna excision repair protein ercc-5). [swissprot;acc:p28715] High confidence 252.873 261.821 1.03539
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

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/