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 2808 to 2857 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
702 vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] Squared 25114 29386 1.1701
703 dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Rooted 51.4945 48.0189 1.07238
limkain b1. [refseq;acc:nm_019081] Ranked 220.438 209.118 1.05413
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Measured 6912.56 7735.12 1.11899
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Squared 25114 29386 1.1701
704 alpha-nac protein. [sptrembl;acc:q9h009] Measured 6912.27 7734.68 1.11898
golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735] Squared 25114 29386 1.1701
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Ranked 220.438 209.118 1.05413
syntaxin 10 (syn10). [swissprot;acc:o60499] Rooted 57.2102 53.3508 1.07234
705 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Ranked 220.438 209.118 1.05413
delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Squared 25114 29386 1.1701
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Measured 6912.09 7734.41 1.11897
syntaxin 6. [swissprot;acc:o43752] Rooted 57.2202 53.3639 1.07226
706 cellular modulator of immune recognition. [refseq;acc:nm_145021] Squared 25114 29386 1.1701
di-ras2. [refseq;acc:nm_017594] Measured 6912.08 7734.39 1.11897
disks large-associated protein 3 (dap-3) (sap90/psd-95-associated protein 3) (sapap3) (psd-95/sap90 binding protein 3) (fragment). [swissprot;acc:o95886] Ranked 220.438 209.118 1.05413
signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Rooted 60.6572 64.9858 1.07136
707 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Measured 5317.78 5944.25 1.11781
kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Ranked 220.438 209.118 1.05413
mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] Rooted 74.8348 80.1352 1.07083
vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Squared 25114 29386 1.1701
708 disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] Ranked 220.438 209.118 1.05413
peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Rooted 74.8348 80.1352 1.07083
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Squared 19970 23366.8 1.1701
z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Measured 5317.78 5944.25 1.11781
709 ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Ranked 220.438 209.118 1.05413
gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Squared 25114 29386 1.1701
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] Rooted 80.4069 86.1018 1.07083
pp1201 protein. [refseq;acc:nm_022152] Measured 5317.78 5944.25 1.11781
710 disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] Ranked 220.438 209.118 1.05413
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Measured 5317.78 5944.25 1.11781
ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Squared 51519.3 44060.4 1.16929
son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Rooted 69.2869 74.1856 1.0707
711 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 58.3914 62.5196
hexaprenyldihydroxybenzoate methyltransferase, mitochondrial precursor (ec 2.1.1.114) (dihydroxyhexaprenylbenzoate methyltransferase) (3,4- dihydroxy-5-hexaprenylbenzoate methyltransferase) (dhhb methyltransferase) (dhhb-mt) (dhhb-mtase). [swissprot;acc:q9nzj6] Squared 25626.4 29950.3 1.16873
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Measured 5317.78 5944.25 1.11781
tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Ranked 232.468 245.048 1.05411
712 atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Squared 25626.4 29950.3 1.16873
ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Ranked 220.431 209.123 1.05407
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Measured 5317.78 5944.25 1.11781
vinculin (metavinculin). [swissprot;acc:p18206] Rooted 62.9163 67.3603 1.07063
713 dendritic cell protein. [refseq;acc:nm_006360] Ranked 223.121 211.685 1.05402
guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] Squared 25626.4 29950.3 1.16873
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Rooted 69.3627 74.2575 1.07057
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Measured 3996.81 4465.61 1.11729
714 dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 5222.71 5834.57 1.11715
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Rooted 61.0082 65.306 1.07045
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Ranked 223.121 211.685 1.05402
vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864] Squared 25904.2 30273.7 1.16868
715 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] Ranked 223.121 211.685 1.05402

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/