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 4358 to 4407 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
2179 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
2189 arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7] Subtracted 5853.67 6136.97 283.3
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610] Divided 5285.03 5033.55 1.04996
2190 glutamate--cysteine ligase regulatory subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs light chain) (glutamate--cysteine ligase modifier subunit). [swissprot;acc:p48507] Subtracted 6822.6 6539.8 282.8
phosducin-like protein (phlp). [swissprot;acc:q13371] Divided 5285.38 5034.86 1.04976
2191 glutamate--cysteine ligase catalytic subunit (ec 6.3.2.2) (gamma- glutamylcysteine synthetase) (gamma-ecs) (gcs heavy chain). [swissprot;acc:p48506] Subtracted 6822.6 6539.8 282.8
replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694] Divided 5285.38 5034.86 1.04976
2192 activin a receptor, type ic; activin receptor-like kinase 7. [refseq;acc:nm_145259] Subtracted 5379.55 5660.25 280.7
replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927] Divided 5285.38 5034.86 1.04976
2193 phosducin (phd) (33 kda phototransducing protein) (meka protein). [swissprot;acc:p20941]
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] Subtracted 5379.49 5660.18 280.69
2194 dna repair protein rad52 homolog. [swissprot;acc:p43351] Divided 5285.38 5034.86 1.04976
neuronal calcium sensor 1 (ncs-1) (frequenin homolog) (frequenin-like protein) (frequenin-like ubiquitous protein). [swissprot;acc:p36610] Subtracted 5379.33 5660 280.67
2195 abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910] 5864.49 6145.14 280.65
ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [swissprot;acc:p49247] Divided 6197.11 6504.93 1.04967
2196 potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459] 6688.64 7020.02 1.04954
quaking isoform 6. [sptrembl;acc:q9p0x9] Subtracted 5864.49 6145.14 280.65
2197 clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675] Divided 5285.79 5036.39 1.04952
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] Subtracted 5379.03 5659.64 280.61
2198 cathepsin l2 precursor (ec 3.4.22.43) (cathepsin v) (cathepsin u). [swissprot;acc:o60911] 5902.26 6181.21 278.95
complement component 1, q subcomponent binding protein, mitochondrial precursor (glycoprotein gc1qbp) (gc1q-r protein) (hyaluronan-binding protein 1) (p32) (p33). [swissprot;acc:q07021] Divided 6344.31 6657.98 1.04944
2199 sirtuin 1; sir2-like 1; sirtuin type 1; sir2alpha; sirtuin silent mating type information regulation 2 homolog 1 (s. cerevisiae). [refseq;acc:nm_012238]
sodium/potassium-transporting atpase alpha-1 chain precursor (ec 3.6.3.9) (sodium pump 1) (na+/k+ atpase 1). [swissprot;acc:p05023] Subtracted 5902.27 6181.21 278.94
2200 cathepsin l precursor (ec 3.4.22.15) (major excreted protein) (mep). [swissprot;acc:p07711]
rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] Divided 5076.73 5326.29 1.04916
2201 cytochrome c. [swissprot;acc:p00001]
sodium/potassium-transporting atpase alpha-3 chain (ec 3.6.3.9) (sodium pump 3) (na+/k+ atpase 3) (alpha(iii)). [swissprot;acc:p13637] Subtracted 5902.27 6181.21 278.94
2202 heparan sulfate 6-o-sulfotransferase 2. [refseq;acc:nm_147174] Divided 5076.73 5326.29 1.04916
sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993] Subtracted 5902.27 6181.21 278.94
2203 candidate tumor suppressor in ovarian cancer 2. [refseq;acc:nm_080822] 4813.13 5091.36 278.23
heparan sulfate 6-o-sulfotransferase; heparan-sulfate 6-sulfotransferase. [refseq;acc:nm_004807] Divided 5076.73 5326.29 1.04916
2204 fatty acid hydroxylase domain containing 1. [refseq;acc:nm_024306]

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/