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 1110 to 1159 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
278 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] Divided 0 11644 10763.4 1.08181
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Subtracted 11107.1 11959.2 852.1
myelin gene expression factor 2. [refseq;acc:nm_016132] 1 235.383 258.476 23.093
279 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Divided 0 10614.2 9812.39 1.08171
histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 1 252.644 228.42 1.10605
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] Subtracted 0 7621.99 8473.85 851.86
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] 1 242.66 265.715 23.055
280 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Divided 0 10620.1 11471.2 1.08014
Subtracted 851.1
metastasis-associated protein mta1. [swissprot;acc:q13330] Divided 1 252.512 228.356 1.10578
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Subtracted 267.208 244.168 23.04
281 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 22.945
60s ribosomal protein l17 (l23). [swissprot;acc:p18621] Divided 241.808 267.335 1.10557
Subtracted 0 11096.8 10251.6 845.2
phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6] Divided 12522.7 13514.5 1.0792
282 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] 1 252.39 228.297 1.10553
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Subtracted 0 10735.1 9891.37 843.73
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] 1 242.159 265.104 22.945
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Divided 0 8095.69 8732.68 1.07868
283 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] Subtracted 1 242.37 265.255 22.885
60s ribosomal protein l11. [swissprot;acc:p39026] Divided 241.828 267.346 1.10552
lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] 0 11107.1 11959.2 1.07672
myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829] Subtracted 10735.1 9891.37 843.73
284 3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8] 12338.7 11512.3 826.4
crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] Divided 1 224.657 203.235 1.10541
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Subtracted 242.686 265.516 22.83
tyrosinase-related gene segment, exon 5 (fragment). [sptrembl;acc:q15677] Divided 0 14898.9 16041.6 1.0767
285 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted 10741.6 9922.33 819.27
dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] Divided 10686 9925.58 1.07661
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Subtracted 1 242.691 265.481 22.79
t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] Divided 224.647 203.242 1.10532
286 60s ribosomal protein l30. [swissprot;acc:p04645] Subtracted 242.593 265.365 22.772
dyskerin (nucleolar protein nap57) (cbf5 homolog). [swissprot;acc:o60832] Divided 0 12228.2 11367.3 1.07573
enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 1 224.633 203.251 1.1052
intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3] Subtracted 0 11431.4 12244.1 812.7
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Divided 1 240.758 266.079 1.10517
far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902] Subtracted 0 10922.9 11731.8 808.9
proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931] Divided 17842.7 16590.3 1.07549
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted 1 225.217 202.459 22.758
288 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Divided 240.758 266.078 1.10517
5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643] 0 14930.6 16053 1.07517
my016 protein. [sptrembl;acc:q9h3k6] Subtracted 5561.19 6366.91 805.72
syntaxin 10 (syn10). [swissprot;acc:o60499] 1 234.691 257.442 22.751
289 anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] 0 10614.2 9812.39 801.81
forkhead box protein g1c (forkhead-related protein fkhl3) (hfk3) (fragment). [swissprot;acc:q14488] Divided 15147.2 14091.9 1.07489
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 1 272.781 246.892 1.10486
syntaxin 6. [swissprot;acc:o43752] Subtracted 234.673 257.414 22.741
290 interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123] Divided 0 15147.2 14091.9 1.07489
ribonucleoside-diphosphate reductase m2 chain (ec 1.17.4.1) (ribonucleotide reductase small chain). [swissprot;acc:p31350] 1 231.969 210.064 1.10428
spectrin alpha chain, brain (spectrin, non-erythroid alpha chain) (alpha-ii spectrin) (fodrin alpha chain). [swissprot;acc:q13813] Subtracted 0 3474 2695 779

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/