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 4308 to 4357 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2154 rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Subtracted 5838.01 6132.35 294.34
2155 centaurin gamma 2. [swissprot;acc:q9upq3] Divided 5701.81 6000.03 1.0523
upstream stimulatory factor 2 (upstream transcription factor 2) (fos-interacting protein) (fip) (major late transcription factor 2). [swissprot;acc:q15853] Subtracted 6373.94 6666.87 292.93
2156 general vesicular transport factor p115 (transcytosis associated protein) (tap) (vesicle docking protein). [swissprot;acc:o60763] Divided 5701.81 6000.03 1.0523
upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415] Subtracted 6374.64 6667.06 292.42
2157 centaurin gamma 1. [swissprot;acc:q99490] Divided 5701.81 6000.03 1.0523
dj718p11.1.2 (novel class ii aminotransferase similar to serine palmotyltransferase (isoform 2)) (fragment). [sptrembl;acc:q9ugb5] Subtracted 6209.77 6501.99 292.22
2158 centaurin gamma 3. [swissprot;acc:q96p47] Divided 5701.81 6000.03 1.0523
histone-lysine n-methyltransferase, h3 lysine-9 specific 2 (ec 2.1.1.43) (histone h3-k9 methyltransferase 2) (h3-k9-hmtase 2) (suppressor of variegation 3-9 homolog 2) (su(var)3-9 homolog 2). [swissprot;acc:q9h5i1] Subtracted 5060.82 5350.93 290.11
2159 eukaryotic translation initiation factor 2 subunit 1 (eukaryotic translation initiation factor 2 alpha subunit) (eif-2-alpha) (eif- 2alpha) (eif-2a). [swissprot;acc:p05198]
serine/threonine-protein kinase receptor r2 precursor (ec 2.7.1.37) (skr2) (activin receptor-like kinase 4) (alk-4) (actr-ib). [swissprot;acc:p36896] Divided 5379.49 5660.18 1.05218
2160 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] 5379.55 5660.25
histone-lysine n-methyltransferase, h3 lysine-9 specific 1 (ec 2.1.1.43) (histone h3-k9 methyltransferase 1) (h3-k9-hmtase 1) (suppressor of variegation 3-9 homolog 1) (su(var)3-9 homolog 1). [swissprot;acc:o43463] Subtracted 5060.82 5350.93 290.11
2161 neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Divided 5379.33 5660 1.05218
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] Subtracted 4102.1 4392.15 290.05
2162 tgf-beta receptor type i precursor (ec 2.7.1.37) (tgfr-1) (tgf-beta type i receptor) (serine/threonine-protein kinase receptor r4) (skr4) (activin receptor-like kinase 5) (alk-5). [swissprot;acc:p36897] Divided 5379.03 5659.64 1.05217
zinc finger protein 277. [swissprot;acc:q9nrm2] Subtracted 4102.1 4392.15 290.05
2163 dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928] Divided 3569.06 3392.22 1.05213
maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5] Subtracted 5247.76 5537.75 289.99
2164 serine palmitoyltransferase 2 (ec 2.3.1.50) (long chain base biosynthesis protein 2) (lcb 2) (serine-palmitoyl-coa transferase 2) (spt 2). [swissprot;acc:o15270] 6196.65 6486.12 289.47
ubiquinone biosynthesis monooxgenase coq6 (ec 1.14.13.-) (cgi-10). [swissprot;acc:q9y2z9] Divided 6952.66 7315.06 1.05212
2165 folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932] Subtracted 4934.48 5223.69 289.21
kynurenine 3-monooxygenase (kynurenine 3-hydroxylase). [refseq;acc:nm_003679] Divided 6952.66 7315.06 1.05212
2166 chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265] Subtracted 5910.12 6199.28 289.16
squalene monooxygenase (ec 1.14.99.7) (squalene epoxidase) (se). [swissprot;acc:q14534] Divided 6952.66 7315.06 1.05212
2167 kinesin-like protein kif13a (kinesin-like protein rbkin). [swissprot;acc:q9h1h9] Subtracted 5910.12 6199.28 289.16
mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001] Divided 3641.62 3461.4 1.05207
2168 conserved oligomeric golgi complex component 2 (low density lipoprotein receptor defect c-complementing protein). [swissprot;acc:q14746] Subtracted 5910.12 6199.28 289.16
hydroxyacid oxidase 1 (ec 1.1.3.15) (haox1) (glycolate oxidase) (gox). [swissprot;acc:q9ujm8] Divided 4561.75 4799.24 1.05206
2169 60s ribosomal protein l5. [swissprot;acc:p46777] 3639.65 3459.64 1.05203
kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Subtracted 5910.12 6199.28 289.16
2170 exonuclease 1 isoform b; rad2 nuclease family member, homolog of s. cerevisiae exonuclease 1. [refseq;acc:nm_006027] Divided 5825.61 6126.74 1.05169
sr rich protein. [refseq;acc:nm_032870] Subtracted 6245.32 6534.23 288.91
2171 diphthamide biosynthesis-like protein 2. [refseq;acc:nm_001384] 4935.84 5224.27 288.43
phd finger protein 9. [refseq;acc:nm_018062] Divided 5825.61 6126.74 1.05169
2172 small optic lobes homolog; small optic lobes, drosophila, homolog of. [refseq;acc:nm_005632]
thioredoxin-like; pkc-interacting cousin of thioredoxin. [refseq;acc:nm_006541] Subtracted 4590.74 4879.11 288.37
2173 epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830] Divided 3641.4 3462.96 1.05153
maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168] Subtracted 5241.34 5529.25 287.91
2174 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] Divided 3641.45 3463.02 1.05152
eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5] Subtracted 5328.73 5616.59 287.86
2175 60s ribosomal protein l23a. [swissprot;acc:p29316] Divided 3642.13 3463.88 1.05146
erythroid differentiation and denucleation factor 1. [swissprot;acc:o60584] Subtracted 5328.73 5616.59 287.86
2176 bardet-biedl syndrome 7 protein isoform a; bbs2-like 1. [refseq;acc:nm_176824]
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] Divided 6674.58 7015.93 1.05114
2177 ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5] Subtracted 5328.73 5616.59 287.86
elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576] Divided 5887.43 6187.82 1.05102
2178 elav-like protein 1 (hu-antigen r) (hur). [swissprot;acc:q15717] 5893.23 6193.33 1.05092
lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [swissprot;acc:p50851] Subtracted 5328.73 5616.59 287.86
2179 elav-like protein 4 (paraneoplastic encephalomyelitis antigen hud) (hu-antigen d). [swissprot;acc:p26378] Divided 5896.51 6196.59 1.05089

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/