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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2832 to 2881 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
708 Rooted peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 74.8348 80.1352 1.07083
709 Measured pp1201 protein. [refseq;acc:nm_022152] 5317.78 5944.25 1.11781
Ranked ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 220.438 209.118 1.05413
Squared gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] 25114 29386 1.1701
Rooted oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] 80.4069 86.1018 1.07083
710 Measured lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 5317.78 5944.25 1.11781
Ranked disks large-associated protein 4 (dap-4) (sap90/psd-95-associated protein 4) (sapap4) (psd-95/sap90 binding protein 4). [swissprot;acc:q9y2h0] 220.438 209.118 1.05413
Squared ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] 51519.3 44060.4 1.16929
Rooted son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] 69.2869 74.1856 1.0707
711 Measured sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] 5317.78 5944.25 1.11781
Ranked tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] 232.468 245.048 1.05411
Squared 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] 25626.4 29950.3 1.16873
Rooted dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 58.3914 62.5196 1.0707
712 Measured sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] 5317.78 5944.25 1.11781
Ranked ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 220.431 209.123 1.05407
Squared atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] 25626.4 29950.3 1.16873
Rooted vinculin (metavinculin). [swissprot;acc:p18206] 62.9163 67.3603 1.07063
713 Measured upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] 3996.81 4465.61 1.11729
Ranked dendritic cell protein. [refseq;acc:nm_006360] 223.121 211.685 1.05402
Squared guanine deaminase (ec 3.5.4.3) (guanase) (guanine aminase) (guanine aminohydrolase) (gah) (p51-nedasin). [swissprot;acc:q9y2t3] 25626.4 29950.3 1.16873
Rooted son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] 69.3627 74.2575 1.07057
714 Measured dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 5222.71 5834.57 1.11715
Ranked potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 223.121 211.685 1.05402
Squared 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] 25904.2 30273.7 1.16868
Rooted histone deacetylase 2 (hd2). [swissprot;acc:q92769] 61.0082 65.306 1.07045
715 Measured dendritic cell protein. [refseq;acc:nm_006360] 6593.17 7364.55 1.117
Ranked 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] 223.121 211.685 1.05402
Squared 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] 25911.5 30281.9 1.16867
Rooted multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 61.0097 65.3071 1.07044
716 Measured potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 6593.17 7364.55 1.117
Ranked cpz gene product. [refseq;acc:nm_003652] 223.121 211.685 1.05402
Squared apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 25911.5 30281.9 1.16867
Rooted dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 61.0098 65.3071 1.07044
717 Measured 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] 6593.17 7364.55 1.117
Ranked carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 223.121 211.685 1.05402
Squared sec13-related protein. [swissprot;acc:p55735] 25911.7 30282.1 1.16867
Rooted histone deacetylase 1 (hd1). [swissprot;acc:q13547] 61.0111 65.3081 1.07043
718 Measured cpz gene product. [refseq;acc:nm_003652] 6593.17 7364.55 1.117
Ranked potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 223.121 211.685 1.05402
Squared 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] 25911.5 30281.9 1.16867
Rooted phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285] 60.7498 65.0218 1.07032
719 Measured carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] 6593.17 7364.55 1.117
Ranked nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 247.769 235.074 1.054
Squared yeast sec31p homolog. [refseq;acc:nm_014933] 25911.7 30282.1 1.16867
Rooted phenylalanine-trna synthetase. [refseq;acc:nm_006567] 60.7498 65.0218 1.07032
720 Measured potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 6593.17 7364.55 1.117
Ranked 60s acidic ribosomal protein p2. [swissprot;acc:p05387] 231.92 244.435 1.05396
Squared vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348] 25911.5 30281.9 1.16867
Rooted jm1 protein. [refseq;acc:nm_014008] 61.5849 65.9155 1.07032
721 Measured syntaxin 7. [swissprot;acc:o15400] 5580.97 6233.52 1.11692

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/