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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1508 to 1557 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
754 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Low confidence 203.246 197.894 1.02704
755 epidermal growth factor receptor pathway substrate 8-like protein 2; eps8-related protein 2; epidermal growth factor receptor pathway substrate 8-related protein 2. [refseq;acc:nm_022772] 206.435 201.001 1.02703
uridine 5'-monophosphate synthase (ump synthase) [includes: orotate phosphoribosyltransferase (ec 2.4.2.10) (oprtase); orotidine 5'- phosphate decarboxylase (ec 4.1.1.23) (ompdecase)]. [swissprot;acc:p11172] High confidence 224.434 235.583 1.04968
756 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]
u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Low confidence 201.703 196.395 1.02703
757 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] High confidence 224.434 235.583 1.04968
epidermal growth factor receptor precursor (ec 2.7.1.112) (receptor protein-tyrosine kinase erbb-1). [swissprot;acc:p00533] Low confidence 211.344 205.788 1.027
758 phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] High confidence 224.434 235.583 1.04968
receptor protein-tyrosine kinase erbb-2 precursor (ec 2.7.1.112) (p185erbb2) (neu proto-oncogene) (c-erbb-2) (tyrosine kinase-type cell surface receptor her2) (mln 19). [swissprot;acc:p04626] Low confidence 211.342 205.787 1.02699
759 n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] 200.18 194.922 1.02697
osteoclast stimulating factor 1. [swissprot;acc:q92882] High confidence 231.809 243.289 1.04952
760 transportin-sr; importin 12. [refseq;acc:nm_012470] Low confidence 191.294 186.27 1.02697
upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] High confidence 246.055 234.458 1.04946
761 homeobox protein nkx-2.3 (homeobox protein nkx-2.3) (homeobox protein nk-2 homolog c). [swissprot;acc:q8tau0] Low confidence 206.052 200.644 1.02695
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] High confidence 213.325 203.303 1.0493
762 cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] 213.256 203.237
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] Low confidence 213.926 208.315 1.02694
763 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 213.929 208.318 1.02693
putative n6-dna-methyltransferase (ec 2.1.1.-) (protein pred28) (m.hsahemk2p). [swissprot;acc:q9y5n5] High confidence 228.78 218.091 1.04901
764 homeobox protein nkx-2.5 (homeobox protein nk-2 homolog e) (cardiac- specific homeobox) (homeobox protein csx). [swissprot;acc:p52952] Low confidence 206.038 200.638 1.02691
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] High confidence 222.082 211.707 1.04901
765 hemk protein homolog (ec 2.1.1.-) (m.hsahemkp). [swissprot;acc:q9y5r4] 229.045 218.343
protein disulfide isomerase a3 precursor (ec 5.3.4.1) (disulfide isomerase er-60) (erp60) (58 kda microsomal protein) (p58) (erp57) (58 kda glucose regulated protein). [swissprot;acc:p30101] Low confidence 204.144 198.795 1.02691
766 cyclin fold protein 1; cyclin-box carrying protein 1. [refseq;acc:nm_145012] 206.437 201.034 1.02688
protein tara (trio-associated repeat on actin) (hrihfb2122). [swissprot;acc:q9h2d6] High confidence 213.804 224.226 1.04875
767 rho interacting protein 3. [refseq;acc:nm_015134] 213.803 224.224 1.04874
swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily b member 1 (integrase interactor 1 protein) (hsnf5) (baf47). [swissprot;acc:q12824] Low confidence 206.437 201.034 1.02688
768 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] High confidence 210.946 221.225 1.04873
ubiquitin-conjugating enzyme e2-32 kda complementing (ec 6.3.2.19) (ubiquitin-protein ligase) (ubiquitin carrier protein) (e2-cdc34). [swissprot;acc:p49427] Low confidence 199.792 194.573 1.02682
769 cab2. [refseq;acc:nm_033419] High confidence 210.946 221.225 1.04873
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Low confidence 198.33 193.155 1.02679
770 dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] High confidence 210.946 221.225 1.04873
orphan nuclear receptor tr4 (orphan nuclear receptor tak1). [swissprot;acc:p49116] Low confidence 206.636 212.168 1.02677
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] High confidence 210.946 221.225 1.04873
synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721] Low confidence 206.636 212.168 1.02677
772 eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] High confidence 210.946 221.225 1.04873
protein phosphatase 1, regulatory (inhibitor) subunit 3b. [refseq;acc:nm_024607] Low confidence 203.48 198.181 1.02674
773 protein containing cxxc domain 2. [refseq;acc:nm_032590] 202.951 208.378
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] High confidence 210.946 221.225 1.04873
774 multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279] 225.996 215.535 1.04854
ubiquitin associated protein 2 isoform 1; ad-012 protein. [refseq;acc:nm_018449] Low confidence 205.905 200.545 1.02673
775 histone deacetylase 2 (hd2). [swissprot;acc:q92769] High confidence 226.003 215.541 1.04854
transcription factor iib. [refseq;acc:nm_013242] Low confidence 205.668 200.313 1.02673
776 dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8] High confidence 225.996 215.535 1.04854
mad1-like 1; mad1 (mitotic arrest deficient, yeast, homolog)-like 1; mitotic-arrest deficient 1, yeast, homolog-like 1; tumor protein p53 inducible protein 9. [refseq;acc:nm_003550] Low confidence 208.017 202.601 1.02673
777 adapter-related protein complex 1 sigma 1c subunit (sigma-adaptin 1c) (adaptor protein complex ap-1 sigma-1c subunit) (golgi adaptor ha1/ap1 adaptin sigma-1c subunit) (clathrin assembly protein complex 1 sigma- 1c small chain) (sigma 1c subunit of ap-1 clathrin). [swissprot;acc:q96pc3] 204.807 199.484 1.02668
histone deacetylase 1 (hd1). [swissprot;acc:q13547] High confidence 225.989 215.53 1.04853
778 sorting nexin 6 (traf4-associated factor 2). [swissprot;acc:q9unh7] 209.191 219.332 1.04848
wd repeat domain 26. [refseq;acc:nm_025160] Low confidence 188.145 183.258 1.02667
779 abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [refseq;acc:nm_005759] 202.48 197.229 1.02662

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
- 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/