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 4208 to 4257 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2104 protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] Divided 6916.14 7295.24 1.05481
2105 3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]
guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] Subtracted 5620.55 5926.71 306.16
2106 mothers against decapentaplegic homolog 2 (smad 2) (mothers against dpp homolog 2) (mad-related protein 2) (hmad-2) (jv18-1) (hsmad2). [swissprot;acc:q15796] 6773.67 7075.51 301.84
zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782] Divided 6916.14 7295.24 1.05481
2107 hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507]
mothers against decapentaplegic homolog 1 (smad 1) (mothers against dpp homolog 1) (mad-related protein 1) (transforming growth factor- beta signaling protein-1) (bsp-1) (hsmad1) (jv4-1). [swissprot;acc:q15797] Subtracted 6773.67 7075.51 301.84
2108 cop9 subunit 6 (mov34 homolog, 34 kd). [refseq;acc:nm_006833]
hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282] Divided 6916.14 7295.24 1.05481
2109 mothers against decapentaplegic homolog 3 (smad 3) (mothers against dpp homolog 3) (mad3) (hmad-3) (mmad3) (jv15-2) (hsmad3). [swissprot;acc:q92940] Subtracted 6773.67 7075.51 301.84
prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674] Divided 6916.14 7295.24 1.05481
2110 histone deacetylase 11 (hd11). [swissprot;acc:q96db2] Subtracted 6773.67 7075.51 301.84
homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786] Divided 6916.14 7295.24 1.05481
2111 ethanolamine kinase-like protein eki2 (flj10761). [swissprot;acc:q9nvf9] Subtracted 6773.67 7075.51 301.84
rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853] Divided 6916.14 7295.24 1.05481
2112 ethanolamine kinase (ec 2.7.1.82) (eki). [swissprot;acc:q9hbu6] Subtracted 6773.67 7075.51 301.84
prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460] Divided 6916.14 7295.24 1.05481
2113 hepatocellular carcinoma susceptibility protein; x 003 protein; hdcmc29p; hspc260; likely ortholog of mouse cd40 ligand-activated specific transcript 3 (clast3). [refseq;acc:nm_020232] Subtracted 6773.67 7075.51 301.84
rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251] Divided 5776.79 6092.77 1.0547
2114 60s ribosomal protein l3-like. [swissprot;acc:q92901] 3617.81 3430.31 1.05466
cop9 constitutive photomorphogenic homolog subunit 5; jun activation domain-binding protein. [refseq;acc:nm_006837] Subtracted 6773.67 7075.51 301.84
2115 60s ribosomal protein l23 (l17). [swissprot;acc:p23131] Divided 3672.49 3482.34 1.0546
mothers against decapentaplegic homolog 9 (smad 9) (mothers against dpp homolog 9) (smad9) (madh6). [swissprot;acc:o15198] Subtracted 6773.67 7075.51 301.84
2116 brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567] Divided 3672.49 3482.34 1.0546
mothers against decapentaplegic homolog 5 (smad 5) (mothers against dpp homolog 5) (smad5) (hsmad5) (jv5-1). [swissprot;acc:q99717] Subtracted 6773.67 7075.51 301.84
2117 ataxin 2-binding protein. [swissprot;acc:q9nwb1] Divided 5778.16 6093.65 1.0546
thioredoxin, mitochondrial precursor (mt-trx) (thioredoxin 2). [swissprot;acc:q99757] Subtracted 6773.67 7075.51 301.84
2118 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] 6568.41 6869.9 301.49
guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774] Divided 5620.55 5926.71 1.05447
2119 blood group rh(d) polypeptide (rhesus d antigen) (rhxiii) (rh polypeptide 2) (rhpii). [swissprot;acc:q02161] Subtracted 6568.51 6869.97 301.46
lamin a/c (70 kda lamin). [swissprot;acc:p02545] Divided 5976.96 6301.73 1.05434
2120 blood group rh(ce) polypeptide (rhesus c/e antigens) (rh30a) (rhixb) (rh polypeptide 1) (rhpi). [swissprot;acc:p18577] Subtracted 6568.51 6869.97 301.46
c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0] Divided 6951.29 7329 1.05434
2121 centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50] 5977.03 6301.76 1.05433
transcription initiation factor tfiid 28 kda subunit (tafii-28) (tafii28) (tfiid subunit p30-beta). [swissprot;acc:q15544] Subtracted 6570.74 6872.1 301.36
2122 centaurin beta 2 (cnt-b2). [swissprot;acc:q15057] Divided 5977.03 6301.76 1.05433
exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Subtracted 5825.61 6126.74 301.13
2123 centaurin beta 1 (cnt-b1). [swissprot;acc:q15027] Divided 5977.03 6301.76 1.05433
phd finger protein 9. [refseq;acc:nm_018062] Subtracted 5825.61 6126.74 301.13
2124 lamin b1. [swissprot;acc:p20700] Divided 5977.09 6301.79 1.05432
small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632] Subtracted 5825.61 6126.74 301.13
2125 rhesus blood group-associated glycoprotein (erythrocyte plasma membrane 50 kda glycoprotein) (rh50a). [swissprot;acc:q02094] 6570.31 6871.29 300.98
ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920] Divided 4806.38 5067 1.05422
2126 40s ribosomal protein s27 (metallopan-stimulin 1) (mps-1). [swissprot;acc:p42677] 4806.33 5066.92
rhesus blood group, b glycoprotein; rh type b glycoprotein. [refseq;acc:nm_020407] Subtracted 6570.74 6871.6 300.86
2127 elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] 5887.43 6187.82 300.39
eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] Divided 5328.73 5616.59 1.05402
2128 erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584]
rh type c glycoprotein. [refseq;acc:nm_016321] Subtracted 6573.3 6873.48 300.18
2129 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824] Divided 5328.73 5616.59 1.05402

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/