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 4008 to 4057 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
1002 SPRY1 sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Ranked 225.167 217.922 1.03325
1003 EXOSC4 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Squared 17541.4 20148.6 1.14863
KIF21A ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590] Rooted 59.2915 62.5118 1.05431
SARS seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591] Measured 5680.76 6220.45 1.095
SPRY2 sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Ranked 225.167 217.922 1.03325
1004 no value sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] 238.725 231.059 1.03318
EXOSC2 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Squared 17541.4 20148.6 1.14863
FOXK2 interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167] Rooted 61.5654 64.9046 1.05424
OSGEP o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807] Measured 5391.64 5903.72 1.09498
1005 ANXA7 annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073] 5780.34 6329.3 1.09497
DYNC1I1 dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576] Ranked 225.448 218.232 1.03307
EXOSC3 exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Squared 17541.4 20148.6 1.14863
XPR1 xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736] Rooted 64.9107 68.4287 1.0542
1006 CASK peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Measured 5707.73 6249.1 1.09485
CPSF3 cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Ranked 116.524 120.375 1.03305
EXOSC5 exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Squared 17541.4 20148.6 1.14863
KIF2A kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139] Rooted 59.3039 62.5177 1.05419
1007 EIF4E eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] Squared 17603.1 20218.5 1.14858
HIF3A hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794] Measured 5707.73 6249.1 1.09485
PNN pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687] Rooted 64.0132 67.4724 1.05404
RALGDS ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967] Ranked 162.055 156.884 1.03296
1008 BAIAP3 bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] Squared 17603.1 20218.5 1.14858
EIF3C eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] Rooted 51.2693 54.0336 1.05392
SIM1 single-minded homolog 1. [swissprot;acc:p81133] Measured 5707.73 6249.1 1.09485
WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] Ranked 243.227 235.475 1.03292
1009 no value dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882] 229.116 221.823 1.03288
RPS24 40s ribosomal protein s24 (s19). [swissprot;acc:p16632] Squared 21492.5 24677.4 1.14819
SYN3 synapsin iii. [swissprot;acc:o14994] Measured 5791.82 6340.86 1.0948
XPO1 exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400] Rooted 58.8768 62.0483 1.05387
1010 no value aspartate beta-hydroxylase isoform b; junctin isoform 1; junctate; aspartyl/asparaginyl-beta-hydroxylase; peptide-aspartate beta-dioxygenase; humbug. [refseq;acc:nm_032468] Measured 5791.82 6340.86 1.0948
CROT peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9] Ranked 217.523 210.648 1.03264
FES proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] Squared 24025.9 27585.7 1.14817
NLK nemo-like kinase; likely ortholog of mouse nemo like kinase. [refseq;acc:nm_016231] Rooted 62.0618 65.4025 1.05383
1011 ERC1 elks protein. [refseq;acc:nm_015064]
HEY1 hairy/enhancer-of-split related with yrpw motif 1 (hairy and enhancer of split related-1) (hesr-1) (cardiovascular helix-loop-helix factor 2) (hes-related repressor protein 2 herp2). [swissprot;acc:q9y5j3] Measured 5791.82 6340.86 1.0948
MOCS2 molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007] Squared 24025.9 27585.7 1.14817
RBL2 retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Ranked 217.026 210.189 1.03253
1012 ABLIM2 actin binding lim protein 2. [refseq;acc:nm_032432] Measured 5791.82 6340.86 1.0948
ANAPC10 anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885] Squared 24025.9 27585.7 1.14817
GORASP2 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] Rooted 74.9231 78.9471 1.05371
RBL1 retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Ranked 217.021 210.185 1.03252
1013 HEATR1 protein bap28. [swissprot;acc:q9h583] 244.312 236.647 1.03239
HEYL hairy/enhancer-of-split related with yrpw motif-like. [refseq;acc:nm_014571] Measured 5791.82 6340.86 1.0948
NDST2 heparin sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.-) (n- hsst) (n-heparin sulfate sulfotransferase) (glucosaminyl n- deacetylase/n-sulfotransferase). [swissprot;acc:p52849] Rooted 58.0289 61.136 1.05354
RPL29 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] Squared 24025.9 27585.7 1.14817
1014 AATF apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] Ranked 243.045 235.422 1.03238
FER proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] Squared 24025.9 27585.7 1.14817
NDST3 n-deacetylase/n-sulfotransferase (heparan glucosaminyl) 3. [refseq;acc:nm_004784] Rooted 58.0289 61.136 1.05354
SYN2 synapsin ii. [swissprot;acc:q92777] Measured 5791.82 6340.86 1.0948
1015 MAGI1 bai1-associated protein 1; ww domain-containing protein 3; atrophin-1 interacting protein 3. [refseq;acc:nm_004742] Ranked 221.73 228.906 1.03236

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/