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 6908 to 6957 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
864 exocyst complex component sec8. [swissprot;acc:q96a65] Rooted Subtracted 63.2983 67.1422 3.8439
glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] Measured 4682.87 4093.05 589.82
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Squared Divided 24242.8 28127.6 1.16025
ring finger protein 44. [refseq;acc:nm_014901] Measured 5595.65 6173.23 1.10322
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Rooted 62.7551 66.6474 1.06202
865 15 kda selenoprotein precursor. [swissprot;acc:o60613] Measured Subtracted 6344.41 6933.36 588.95
alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766] Squared 26583.7 30425.2 3841.5
asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243] Rooted Divided 62.7551 66.6474 1.06202
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Subtracted 62.2332 58.3925 3.8407
phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986] Measured Divided 5595.65 6173.23 1.10322
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Squared 24242.8 28127.6 1.16025
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Ranked 211.961 203.814 1.03997
zinc finger protein 174 (aw-1). [swissprot;acc:q15697] Subtracted 269.963 278.239 8.276
866 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Squared Divided 24242.8 28127.6 1.16025
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642] Rooted Subtracted 62.5007 58.6648 3.8359
esterase d (ec 3.1.1.1). [swissprot;acc:p10768] Squared 26583.7 30425.2 3841.5
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Measured 4510.61 5098.74 588.13
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979] Rooted Divided 51.8306 55.0247 1.06163
ring finger protein 38. [refseq;acc:nm_022781] Measured 5595.65 6173.23 1.10322
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Ranked 221.306 212.806 1.03994
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Subtracted 269.96 278.232 8.272
867 40s ribosomal protein s3a. [swissprot;acc:p49241] Divided 225.689 234.674 1.03981
mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95] Rooted 61.668 65.4526 1.06137
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Squared 24242.8 28127.6 1.16025
phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569] Measured 5595.65 6173.23 1.10322
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401] Subtracted 6545.19 7132.89 587.7
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Rooted 64.1165 67.9451 3.8286
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Squared 19263.3 23092.3 3829
zinc finger protein 18 (zinc finger protein kox11) (fragment). [swissprot;acc:p17022] Ranked 269.956 278.223 8.267
868 biotin--protein ligase (ec 6.3.4.-) (biotin apo-protein ligase) [includes: biotin--[methylmalonyl-coa-carboxyltransferase] ligase (ec 6.3.4.9); biotin--[propionyl-coa-carboxylase [atp-hydrolyzing]] ligase (ec 6.3.4.10) (holocarboxylase synthetase) (hcs); biotin--[methylcrotonoyl-coa-carboxylase] ligase (ec 6.3.4.11); biotin--[acetyl-coa-carboxylase] ligase (ec 6.3.4.15)]. [swissprot;acc:p50747] Measured 5607.43 6194.98 587.55
diphosphomevalonate decarboxylase (ec 4.1.1.33) (mevalonate pyrophosphate decarboxylase) (mevalonate (diphospho)decarboxylase). [swissprot;acc:p53602] Ranked Divided 233.298 242.571 1.03975
keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191] Squared 31099.4 36082.4 1.16023
mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3] Rooted 61.668 65.4526 1.06137
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Subtracted 64.1184 67.9467 3.8283
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Measured Divided 5595.65 6173.23 1.10322
syntaxin 6. [swissprot;acc:o43752] Squared Subtracted 26720.4 30548.3 3827.9
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Ranked 269.956 278.223 8.267
869 atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Measured Divided 5595.65 6173.23 1.10322
exocyst complex component sec8. [swissprot;acc:q96a65] Ranked 217.762 209.449 1.03969
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567] Rooted 61.668 65.4526 1.06137
protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316] Subtracted 100.26 96.4491 3.8109
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456] Measured 6540.61 7127.41 586.8
segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Squared Divided 20273.1 23521.2 1.16022
syntaxin 10 (syn10). [swissprot;acc:o60499] Subtracted 26702.8 30522.5 3819.7
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] Ranked 269.955 278.221 8.266
870 dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Squared 24856.2 28661.3 3805.1
mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [swissprot;acc:p53778] Rooted Divided 84.6378 89.8201 1.06123
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Measured 5595.65 6173.23 1.10322
serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549] Subtracted 6390.28 6973.08 582.8
signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240] Squared Divided 21086.3 24464.1 1.16019

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/