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 4230 to 4279 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2115 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
elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] Subtracted 5893.23 6193.33 300.1
2130 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Divided 5328.73 5616.59 1.05402
elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] Subtracted 5896.51 6196.59 300.08
2131 elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] 5900.25 6200.24 299.99
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Divided 5328.73 5616.59 1.05402
2132 protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]
ubiquitin-conjugating enzyme e2 g2 (ec 6.3.2.19) (ubiquitin-protein ligase g2) (ubiquitin carrier protein g2). [swissprot;acc:p56554] Subtracted 6486.84 6786.23 299.39
2133 38 kda fk-506 binding protein homolog (fkbpr38) (fk506-binding protein 8). [swissprot;acc:q14318]
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Divided 5328.73 5616.59 1.05402
2134 gcn5-like protein 1 (rt14 protein). [swissprot;acc:p78537] Subtracted 8154.48 8453.84 299.36
putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580] Divided 5328.73 5616.59 1.05402
2135 exocyst complex component sec6. [swissprot;acc:o60645] 7387.42 7785.45 1.05388
transcription factor-like protein mrg15 (morf-related gene 15 protein) (mortality factor 4-like 1) (msl3-1 protein) (hspc008/hspc061). [swissprot;acc:q9ubu8] Subtracted 5045.67 5344.06 298.39
2136 60s ribosomal protein l19. [swissprot;acc:p14118] Divided 3687.49 3499.2 1.05381
cug triplet repeat rna-binding protein 1 (cug-bp1) (rna-binding protein brunol-2) (deadenylation factor cug-bp) (50 kda nuclear polyadenylated rna-binding protein) (eden-bp). [swissprot;acc:q92879] Subtracted 5875.13 6173.41 298.28
2137 cug triplet repeat, rna binding protein 2; elav-type rna-binding protein; cug triplet repeat,rna-binding protein 2; cug triplet repeat, rna-binding protein 2; neuroblastoma apoptosis-related rna-binding protein. [refseq;acc:nm_006561] 5875.11 6173.39
sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822] Divided 5859.1 6173.7 1.05369
2138 centaurin gamma 2. [swissprot;acc:q9upq3] Subtracted 5701.81 6000.03 298.22
oxidation resistance 1. [refseq;acc:nm_181354] Divided 5859.1 6173.7 1.05369
2139 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Subtracted 5701.81 6000.03 298.22
lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572] Divided 5859.1 6173.7 1.05369
2140 centaurin gamma 1. [swissprot;acc:q99490] Subtracted 5701.81 6000.03 298.22

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/