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 Hugo description Value Type Interaction Map Network Comparison Type Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1812 to 1861 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
red
green
network_comparison
906 RSL1D1 pbk1 protein. [sptrembl;acc:o76021] Subtracted 243.312 235.353 7.959
907 JUP junction plakoglobin (desmoplakin iii). [swissprot;acc:p14923] Divided 223.906 215.653 1.03827
MTRF1 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Subtracted 225.976 218.017 7.959
908 no value tax interaction protein 1. [refseq;acc:nm_014604] Divided 223.906 215.653 1.03827
ZNF547 sedlin. [swissprot;acc:o14582] Subtracted 129.219 121.261 7.958
909 no value synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
SEPT1 septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Divided 142.077 136.846 1.03823
910 no value uba/ubx 33.3 kda protein. [swissprot;acc:q04323] 217.168 209.207 1.03805
TRAPPC3 bet3 homolog. [swissprot;acc:o43617] Subtracted 129.219 121.261 7.958
911 no value ero1-like. [refseq;acc:nm_014584] Divided 217.168 209.207 1.03805
MPDU1 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Subtracted 225.955 218.015 7.94
912 MTRF1L mitochondrial translational release factor 1-like. [refseq;acc:nm_019041] 225.939 218.013 7.926
WDR3 wd-repeat protein 3. [swissprot;acc:q9unx4] Divided 243.896 234.96 1.03803
913 DDX52 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] Subtracted 243.297 235.373 7.924
TGS1 prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831] Divided 210.863 218.878 1.03801
914 no value guanine nucleotide-binding protein beta subunit-like protein 12.3 (p205) (receptor of activated protein kinase c 1) (rack1) (receptor for activated c kinase). [swissprot;acc:p25388] Subtracted 237.558 229.677 7.881
GOPC pdz/coiled-coil domain binding partner for the rho-family gtpase tc10; fused in glioblastoma; golgi associated pdz and coiled-coil motif containing protein; cftr-associated ligand. [refseq;acc:nm_020399] Divided 210.863 218.878 1.03801
915 TRMU trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 146.036 140.692 1.03798
ZRF1 zuotin related factor-1 (m-phase phosphoprotein 11). [swissprot;acc:q99543] Subtracted 237.558 229.677 7.881
916 no value histone h4. [swissprot;acc:p02304] 227.765 219.902 7.863
HAO2 hydroxyacid oxidase 2 (ec 1.1.3.15) (haox2) ((s)-2-hydroxy-acid oxidase, peroxisomal) (long chain alpha-hydroxy acid oxidase) (long- chain l-2-hydroxy acid oxidase). [swissprot;acc:q9nyq3] Divided 232.512 241.288 1.03774
917 CDC73 parafibromin. [refseq;acc:nm_024529] 239.704 230.991 1.03772
DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Subtracted 86.7483 78.8995 7.8488
918 IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 217.942 210.139 7.803
SORBS1 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Divided 212.952 205.292 1.03731
919 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted 217.942 210.139 7.803
MDN1 midasin (midas-containing protein). [swissprot;acc:q9nu22] Divided 237.218 228.698 1.03725
920 BRCA1 breast cancer type 1 susceptibility protein. [swissprot;acc:p38398] Subtracted 216.501 224.27 7.769
DEAF1 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] Divided 236.741 245.547 1.0372
921 RIOK1 rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480]
WDR46 wd-repeat protein bing4. [swissprot;acc:o15213] Subtracted 243.227 235.475 7.752
922 MARK1 map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650] Divided 236.741 245.547 1.0372
PEF1 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Subtracted 215.665 207.942 7.723
923 HPRT1 hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] 193.114 185.412 7.702
MARK2 map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954] Divided 236.741 245.547 1.0372
924 no value sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633] Subtracted 238.725 231.059 7.666
SPO11 meiotic recombination protein spo11. [swissprot;acc:q9y5k1] Divided 236.741 245.547 1.0372
925 HEATR1 protein bap28. [swissprot;acc:q9h583] Subtracted 244.312 236.647 7.665
PEF1 pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392] Divided 215.665 207.942 1.03714
926 IMMP2L imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] 217.942 210.139 1.03713
SORBS1 ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Subtracted 212.952 205.292 7.66
927 no value microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Divided 217.942 210.139 1.03713
SF3A3 splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Subtracted 220.246 212.618 7.628
928 MTRF1 peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570] Divided 225.976 218.017 1.03651
SF3A1 splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Subtracted 220.246 212.618 7.628
929 AATF apoptosis antagonizing transcription factor. [refseq;acc:nm_012138] 243.045 235.422 7.623
MPDU1 mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352] Divided 225.955 218.015 1.03642
930 PDCD5 programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737] Subtracted 233.402 225.782 7.62
PKM2 pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618] Divided 231.357 239.778 1.0364
931 BHLHB4 ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] 159.13 164.917 1.03637

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/