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 2851 to 2900 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
Interaction Map
red
green
network_comparison
713 elongation factor 1-delta (ef-1-delta) (antigen ny-co-4). [swissprot;acc:p29692] EEF1D Subtracted Low confidence 203.552 198.081 5.471
lipopolysaccharide-binding protein precursor (lbp). [swissprot;acc:p18428] LBP High confidence 224.434 235.583 11.149
714 microsomal signal peptidase 25 kda subunit (ec 3.4.-.-) (spase 25 kda subunit) (spc25). [swissprot;acc:q15005] SPCS2
pap-1 binding protein. [refseq;acc:nm_031288] ZNHIT4 Low confidence 213.16 218.629 5.469
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436] CPXM2 Divided High confidence 223.121 211.685 1.05402
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] SEPT8 Low confidence 152.572 148.47 1.02763
715 carboxypeptidase n catalytic chain precursor (ec 3.4.17.3) (arginine carboxypeptidase) (kininase 1) (serum carboxypeptidase n) (scpn) (anaphylatoxin inactivator) (plasma carboxypeptidase b). [swissprot;acc:p15169] CPN1 High confidence 223.121 211.685 1.05402
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] POLE Subtracted Low confidence 204.279 198.814 5.465
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] GARS Divided 203.107 197.646 1.02763
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] UMPS Subtracted High confidence 224.434 235.583 11.149
716 cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294] CLPTM1
cpz gene product. [refseq;acc:nm_003652] CPZ Divided 223.121 211.685 1.05402
elongation factor 1-delta (ef-1-delta) (antigen ny-co-4). [swissprot;acc:p29692] EEF1D Low confidence 203.552 198.081 1.02762
repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273] no value Subtracted 199.669 194.204 5.465
717 bactericidal permeability-increasing protein precursor (bpi) (cap 57). [swissprot;acc:p17213] BPI High confidence 224.434 235.583 11.149
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] CPE Divided 223.121 211.685 1.05402
epidermal growth factor receptor pathway substrate 8-like protein 1 isoform c; epidermal growth factor receptor pathway substrate 8-related protein 1; eps8-related protein 1. [refseq;acc:nm_139204] EPS8L1 Subtracted Low confidence 206.474 201.013 5.461
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] BTF3 Divided 204.133 198.652 1.02759
718 arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143] ARPC1B 201.612 196.213 1.02752
glycyl-trna synthetase (ec 6.1.1.14) (glycine--trna ligase) (glyrs). [swissprot;acc:p41250] GARS Subtracted 203.107 197.646 5.461
phospholipid transfer protein precursor (lipid transfer protein ii). [swissprot;acc:p55058] PLTP High confidence 224.434 235.583 11.149
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3] CPXM1 Divided 223.121 211.685 1.05402
719 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] APEX2 Subtracted Low confidence 202.569 197.109 5.46
deoxycytidylate deaminase (ec 3.5.4.12) (dcmp deaminase). [swissprot;acc:p32321] DCTD High confidence 230.516 241.641 11.125
nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567] NOL5A Divided 247.769 235.074 1.054
stip1 homology and u-box containing protein 1; serologically defined colon cancer antigen 7; carboxy terminus of hsp70p-interacting protein; heat shock protein a binding protein 2 (c-terminal). [refseq;acc:nm_005861] STUB1 Low confidence 199.172 193.841 1.0275
720 60s acidic ribosomal protein p2. [swissprot;acc:p05387] RPLP2 High confidence 231.92 244.435 1.05396
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] POLE Low confidence 204.279 198.814 1.02749
epidermal growth factor receptor kinase substrate eps8. [swissprot;acc:q12929] EPS8 Subtracted 206.469 201.011 5.458
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] TREH High confidence 217.952 206.902 11.05
721 asc-1 complex subunit p100. [refseq;acc:nm_032204] ASCC2 Low confidence 211.636 206.184 5.452
exocyst complex component sec10 (hsec10). [swissprot;acc:o00471] EXOC5 Divided High confidence 214.765 203.8 1.0538
Subtracted 10.965
sorting nexin 16. [swissprot;acc:p57768] SNX16 Divided Low confidence 203.411 197.971 1.02748
722 glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530] YEATS4 Subtracted 198.424 192.974 5.45
igf-ii mrna-binding protein 1. [refseq;acc:nm_006546] IGF2BP1 Divided 205.571 200.075 1.02747
neuroepithelial cell transforming gene 1; guanine nucleotide regulatory protein (oncogene); rho guanine nucleotide exchange factor (gef) 8. [refseq;acc:nm_005863] NET1 Subtracted High confidence 244.447 233.508 10.939
trehalase precursor (ec 3.2.1.28) (alpha,alpha-trehalase) (alpha,alpha-trehalose glucohydrolase). [swissprot;acc:o43280] TREH Divided 217.952 206.902 1.05341
723 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] no value 244.842 232.577 1.05274
poly(a)-specific ribonuclease (deadenylation nuclease); deadenylation nuclease. [refseq;acc:nm_002582] PARN Low confidence 203.779 198.331 1.02747
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 Subtracted High confidence 244.447 233.508 10.939
ribonuclease h1 (ec 3.1.26.4) (rnase h1) (ribonuclease h type ii). [swissprot;acc:o60930] RNASEH1 Low confidence 206.457 201.008 5.449
724 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] ACY1 Divided 201.765 196.371 1.02747
dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] no value High confidence 244.842 232.577 1.05274
down-regulated in metastasis. [refseq;acc:nm_014503] UTP20 Subtracted 244.447 233.508 10.939
poly(a)-specific ribonuclease (deadenylation nuclease); deadenylation nuclease. [refseq;acc:nm_002582] PARN Low confidence 203.779 198.331 5.448
725 igf-ii mrna-binding protein 3; kh domain containing protein overexpressed in cancer. [refseq;acc:nm_006547] IGF2BP3 Divided 205.563 200.075 1.02743
iron-responsive element binding protein 1 (ire-bp 1) (iron regulatory protein 1) (irp1) (ferritin repressor protein) (aconitate hydratase) (ec 4.2.1.3) (citrate hydro-lyase) (aconitase). [swissprot;acc:p21399] ACO1 Subtracted 200.577 195.136 5.441
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] MVK Divided High confidence 235.296 247.673 1.0526
solute carrier family 35, member b1; udp-galactose transporter related. [refseq;acc:nm_005827] SLC35B1 Subtracted 214.679 225.568 10.889

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/