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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2827 to 2876 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
707 RPUSD2 Measured c18b11 homolog (44.9kd). [refseq;acc:nm_152260] 5317.78 5944.25 1.11781
TOMM20 Rooted mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388] 74.8348 80.1352 1.07083
708 no value Ranked disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6] 220.438 209.118 1.05413
PEX19 Rooted peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] 74.8348 80.1352 1.07083
TMBIM4 Measured z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] 5317.78 5944.25 1.11781
TPI1 Squared triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] 19970 23366.8 1.1701
709 FTL Ranked ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] 220.438 209.118 1.05413
SGCG Squared gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] 25114 29386 1.1701
SLC15A1 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
TMBIM1 Measured pp1201 protein. [refseq;acc:nm_022152] 5317.78 5944.25 1.11781
710 DLGAP4 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
FAIM2 Measured lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 5317.78 5944.25 1.11781
RNF25 Squared ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] 51519.3 44060.4 1.16929
SOS2 Rooted son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] 69.2869 74.1856 1.0707
711 no value 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
COQ3 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
DYNC1I2 Rooted dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] 58.3914 62.5196 1.0707
YARS Ranked tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] 232.468 245.048 1.05411
712 ATP5S Squared atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] 25626.4 29950.3 1.16873
FTHL17 Ranked ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] 220.431 209.123 1.05407
SREBF1 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
VCL Rooted vinculin (metavinculin). [swissprot;acc:p18206] 62.9163 67.3603 1.07063
713 EIF3M Ranked dendritic cell protein. [refseq;acc:nm_006360] 223.121 211.685 1.05402
GDA 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
NAT10 Measured upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] 3996.81 4465.61 1.11729
SOS1 Rooted son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] 69.3627 74.2575 1.07057
714 no value 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
Rooted histone deacetylase 2 (hd2). [swissprot;acc:q92769] 61.0082 65.306 1.07045
ATP6V1F 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
CPXM2 Ranked potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 223.121 211.685 1.05402
715 no value 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
CPN1 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
EIF3M Measured dendritic cell protein. [refseq;acc:nm_006360] 6593.17 7364.55 1.117
MCFD2 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 no value dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] 61.0098
API5 Squared apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595] 25911.5 30281.9 1.16867
CPXM2 Measured potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] 6593.17 7364.55 1.117
CPZ Ranked cpz gene product. [refseq;acc:nm_003652] 223.121 211.685 1.05402
717 CPE carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870]
CPN1 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
HDAC1 Rooted histone deacetylase 1 (hd1). [swissprot;acc:q13547] 61.0111 65.3081 1.07043
SEC13 Squared sec13-related protein. [swissprot;acc:p55735] 25911.7 30282.1 1.16867
718 ATP6V1G3 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
CPXM1 Ranked potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] 223.121 211.685 1.05402
CPZ Measured cpz gene product. [refseq;acc:nm_003652] 6593.17 7364.55 1.117
FARSA 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 CPE 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
FARS2 Rooted phenylalanine-trna synthetase. [refseq;acc:nm_006567] 60.7498 65.0218 1.07032
NOL5A Ranked nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] 247.769 235.074 1.054
SEC31A Squared yeast sec31p homolog. [refseq;acc:nm_014933] 25911.7 30282.1 1.16867

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
- Hugo is the HGNC identifier if it exists
- 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/