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 4327 to 4376 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
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] Subtracted 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
protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1] Subtracted 5328.73 5616.59 287.86
2180 elav-like protein 2 (hu-antigen b) (hub) (elav-like neuronal protein 1) (nervous system-specific rna binding protein hel-n1). [swissprot;acc:q12926] Divided 5900.25 6200.24 1.05084
eukaryotic translation initiation factor 3 subunit 6 interacting protein (hspc021/hspc025). [swissprot;acc:q9y262] Subtracted 5328.73 5616.59 287.86
2181 putative rna-binding protein 7 (rna binding motif protein 7). [swissprot;acc:q9y580]
triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938] Divided 4915.05 5164.75 1.0508
2182 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] 5875.13 6173.41 1.05077
ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636] Subtracted 6480.27 6765.81 285.54
2183 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] Divided 5875.11 6173.39 1.05077
ral-a exchange factor ralgps2. [refseq;acc:nm_152663] Subtracted 6480.27 6765.81 285.54
2184 rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [swissprot;acc:q9h0z9] Divided 5838.01 6132.35 1.05042
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] Subtracted 6480.27 6765.81 285.54
2185 60s ribosomal protein l12. [swissprot;acc:p30050] Divided 3586.32 3414.42 1.05035
putative pre-mrna splicing factor rna helicase (atp-dependent rna helicase #3) (deah-box protein 16). [swissprot;acc:o60231] Subtracted 6362.48 6647.42 284.94
2186 60s ribosomal protein l12 like protein. [sptrembl;acc:o60886] Divided 3586.3 3414.4 1.05035
t54 protein. [swissprot;acc:q92917] Subtracted 6362.48 6647.42 284.94
2187 dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02] Divided 3586.31 3414.41 1.05035
m-phase inducer phosphatase 1 (ec 3.1.3.48) (dual specificity phosphatase cdc25a). [swissprot;acc:p30304] Subtracted 4521 4805.16 284.16
2188 nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [refseq;acc:nm_014062] 4689.78 4973.44 283.66
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470] Divided 6682.7 7018.29 1.05022

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/