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.


Navigation/Query Panel:
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 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
Hugo
description
Value Type
red
green
network_comparison
702 SH3GL3 sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [swissprot;acc:q99963] Measured 7067.46 7909.27 1.11911
703 no value nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] 6912.56 7735.12 1.11899
KIAA0430 limkain b1. [refseq;acc:nm_019081] Ranked 220.438 209.118 1.05413
POLR2C 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
SGCZ sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Squared 25114 29386 1.1701
704 no value alpha-nac protein. [sptrembl;acc:q9h009] Measured 6912.27 7734.68 1.11898
putative adenosylhomocysteinase 3 (ec 3.3.1.1) (s-adenosyl-l- homocysteine hydrolase) (adohcyase). [swissprot;acc:q96hn2] Ranked 220.438 209.118 1.05413
ACBD3 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
STX10 syntaxin 10 (syn10). [swissprot;acc:o60499] Rooted 57.2102 53.3508 1.07234
705 CREG1 cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851] Ranked 220.438 209.118 1.05413
DIRAS1 small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Measured 6912.09 7734.41 1.11897
SGCD delta-sarcoglycan (sg-delta) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q92629] Squared 25114 29386 1.1701
STX6 syntaxin 6. [swissprot;acc:o43752] Rooted 57.2202 53.3639 1.07226
706 DIRAS2 di-ras2. [refseq;acc:nm_017594] Measured 6912.08 7734.39 1.11897
DLGAP3 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
MARCH8 cellular modulator of immune recognition. [refseq;acc:nm_145021] Squared 25114 29386 1.1701
SRP68 signal recognition particle 68 kda protein (srp68). [swissprot;acc:q9uhb9] Rooted 60.6572 64.9858 1.07136
707 ATP6V0B vacuolar atp synthase 21 kda proteolipid subunit (ec 3.6.3.14) (hatpl). [swissprot;acc:q99437] Squared 25114 29386 1.1701
KNG1 kininogen precursor (alpha-2-thiol proteinase inhibitor) [contains: bradykinin]. [swissprot;acc:p01042] Ranked 220.438 209.118 1.05413
RPUSD2 c18b11 homolog (44.9kd). [refseq;acc:nm_152260] Measured 5317.78 5944.25 1.11781
TOMM20 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
708 no value 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
PEX19 peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855] Rooted 74.8348 80.1352 1.07083
TMBIM4 z-protein (protein cgi-119) (s1r protein). [swissprot;acc:q9hc24] Measured 5317.78 5944.25 1.11781
TPI1 triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Squared 19970 23366.8 1.1701
709 FTL ferritin light chain (ferritin l subunit). [swissprot;acc:p02792] Ranked 220.438 209.118 1.05413
SGCG gamma-sarcoglycan (gamma-sg) (35 kda dystrophin-associated glycoprotein) (35dag). [swissprot;acc:q13326] Squared 25114 29386 1.1701
SLC15A1 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
TMBIM1 pp1201 protein. [refseq;acc:nm_022152] Measured 5317.78 5944.25 1.11781
710 DLGAP4 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
FAIM2 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Measured 5317.78 5944.25 1.11781
RNF25 ring finger protein 25 (ec 6.3.2.-). [swissprot;acc:q96bh1] Squared 51519.3 44060.4 1.16929
SOS2 son of sevenless protein homolog 2 (sos-2). [swissprot;acc:q07890] Rooted 69.2869 74.1856 1.0707
711 no value 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
COQ3 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
DYNC1I2 dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409] Rooted 58.3914 62.5196 1.0707
YARS tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577] Ranked 232.468 245.048 1.05411
712 ATP5S atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766] Squared 25626.4 29950.3 1.16873
FTHL17 ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8] Ranked 220.431 209.123 1.05407
SREBF1 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
VCL vinculin (metavinculin). [swissprot;acc:p18206] Rooted 62.9163 67.3603 1.07063
713 EIF3M dendritic cell protein. [refseq;acc:nm_006360] Ranked 223.121 211.685 1.05402
GDA 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
NAT10 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] Measured 3996.81 4465.61 1.11729
SOS1 son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Rooted 69.3627 74.2575 1.07057
714 no value dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] Measured 5222.71 5834.57 1.11715
histone deacetylase 2 (hd2). [swissprot;acc:q92769] Rooted 61.0082 65.306 1.07045
ATP6V1F 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
CPXM2 potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] Ranked 223.121 211.685 1.05402
715 no value 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

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/