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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1525 to 1574 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
red
green
network_comparison
763 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] no value Subtracted 224.244 234.511 10.267
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] N6AMT1 Divided 228.78 218.091 1.04901
764 leukocyte elastase inhibitor (lei) (monocyte/neutrophil elastase inhibitor) (m/nei) (ei). [swissprot;acc:p30740] SERPINB1 Subtracted 224.244 234.511 10.267
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] PRPF3 Divided 222.082 211.707 1.04901
765 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] EIF3B Subtracted 243.067 232.805 10.262
hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] HEMK1 Divided 229.045 218.343 1.04901
766 protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] TRIOBP 213.804 224.226 1.04875
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] SNX6 Subtracted 209.191 219.332 10.141
767 dna-directed rna polymerase ii 14.5 kda polypeptide (ec 2.7.7.6) (rpb9) (rpb14.5). [swissprot;acc:p36954] POLR2I 228.563 238.668 10.105
rho interacting protein 3. [refseq;acc:nm_015134] no value Divided 213.803 224.224 1.04874
768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] DNAJB4 210.946 221.225 1.04873
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] CBLB Subtracted 213.325 203.303 10.022
769 cab2. [refseq;acc:nm_033419] PERLD1 Divided 210.946 221.225 1.04873
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] CBL Subtracted 213.256 203.237 10.019
770 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] DNAJB5 Divided 210.946 221.225 1.04873
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Subtracted 59 49 10
771 dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] DNAJB1 Divided 210.946 221.225 1.04873
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC Subtracted 59 49 10
772 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] ETF1 Divided 210.946 221.225 1.04873
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB Subtracted 59 49 10
773 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] VPS52 Divided 210.946 221.225 1.04873
774 mitochondrial 28s ribosomal protein s2 (mrp-s2) (cgi-91). [swissprot;acc:q9y399] MRPS2 Subtracted 221.716 231.501 9.785
multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] MCFD2 Divided 225.996 215.535 1.04854
775 histone deacetylase 2 (hd2). [swissprot;acc:q92769] no value 226.003 215.541
u3 snornp protein 4 homolog. [refseq;acc:nm_033416] IMP4 Subtracted 221.676 231.453 9.777
776 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] no value Divided 225.996 215.535 1.04854
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] SQSTM1 Subtracted 221.965 212.404 9.561
777 histone deacetylase 1 (hd1). [swissprot;acc:q13547] HDAC1 Divided 225.989 215.53 1.04853
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] SCP2 Subtracted 221.965 212.404 9.561
778 beta-catenin (pro2286). [swissprot;acc:p35222] CTNNB1 224.445 214.894 9.551
sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] SNX6 Divided 209.191 219.332 1.04848
779 deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] DCTD 230.516 241.641 1.04826
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [refseq;acc:nm_004562] PARK2 Subtracted 231.734 222.222 9.512
780 dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584] POLR2F Divided 232.762 243.933 1.04799
hepatoma-derived growth factor-related protein 2. [refseq;acc:nm_032631] no value Subtracted 231.734 222.222 9.512
781 cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]
ribosomal protein p0-like protein; 60s acidic ribosomal protein po; ribosomal protein, large, p0-like. [refseq;acc:nm_016183] MRTO4 Divided 245.84 257.636 1.04798
782 pc4 and sfrs1 interacting protein 2; pc4 and sfrs1 interacting protein 1; transcriptional coactivator p52/p75. [refseq;acc:nm_033222] PSIP1 Subtracted 231.734 222.222 9.512
translin. [swissprot;acc:q15631] no value Divided 224.385 235.131 1.04789
783 60s ribosomal protein l8. [swissprot;acc:p25120] RPL8 Subtracted 231.734 222.222 9.512
translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598] TSNAX Divided 224.385 235.131 1.04789
784 hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858] HDGF Subtracted 231.734 222.222 9.512
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710] PQBP1 Divided 224.385 235.131 1.04789
785 neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] NET1 244.447 233.508 1.04685
pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574] HDGFL1 Subtracted 231.734 222.222 9.512
786 probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196] DDX6
rho guanine nucleotide exchange factor 3; rhogef protein; 59.8 kda protein; exchange factor found in platelets and leukemic and neuronal tissues, xpln. [refseq;acc:nm_019555] ARHGEF3 Divided 244.447 233.508 1.04685
787 down-regulated in metastasis. [refseq;acc:nm_014503] UTP20
rw1 protein (fragment). [swissprot;acc:q92545] TMEM131 Subtracted 231.734 222.222 9.512

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/