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 2830 to 2879 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
708 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
dendritic cell protein. [refseq;acc:nm_006360] Measured 6593.17 7364.55 1.117
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] Rooted 61.0097 65.3071 1.07044
vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670] Squared 25911.5 30281.9 1.16867
716 apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
cpz gene product. [refseq;acc:nm_003652] Ranked 223.121 211.685 1.05402
dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] Rooted 61.0098 65.3071 1.07044
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Measured 6593.17 7364.55 1.117
717 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Ranked 223.121 211.685 1.05402
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] Measured 6593.17 7364.55 1.117
histone deacetylase 1 (hd1). [swissprot;acc:q13547] Rooted 61.0111 65.3081 1.07043
sec13-related protein. [swissprot;acc:p55735] Squared 25911.7 30282.1 1.16867
718 cpz gene product. [refseq;acc:nm_003652] Measured 6593.17 7364.55 1.117
phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] Rooted 60.7498 65.0218 1.07032
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Ranked 223.121 211.685 1.05402
vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4] Squared 25911.5 30281.9 1.16867
719 carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Measured 6593.17 7364.55 1.117
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] Ranked 247.769 235.074 1.054
phenylalanine-trna synthetase. [refseq;acc:nm_006567] Rooted 60.7498 65.0218 1.07032
yeast sec31p homolog. [refseq;acc:nm_014933] Squared 25911.7 30282.1 1.16867
720 60s acidic ribosomal protein p2. [swissprot;acc:p05387] Ranked 231.92 244.435 1.05396
jm1 protein. [refseq;acc:nm_014008] Rooted 61.5849 65.9155 1.07032
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] Measured 6593.17 7364.55 1.117

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/