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 525 to 574 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
263 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Divided 219.421 196.978 1.11394
protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530] Subtracted 242.14 265.696 23.556
264 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 243.24 266.796
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Divided 219.421 196.978 1.11394
265 60s ribosomal protein l9. [swissprot;acc:p32969] Subtracted 240.243 263.798 23.555
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Divided 225.217 202.459 1.11241
266 ribosomal protein l10-like protein. [refseq;acc:nm_080746] Subtracted 243.12 266.662 23.542
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Divided 241.07 267.88 1.11121
267 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] Subtracted 243.12 266.661 23.541
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Divided 241.07 267.88 1.11121
268 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 271.016 244.167 1.10996
protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678] Subtracted 241.625 265.136 23.511
269 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Divided 241.373 267.352 1.10763
270 40s ribosomal protein s3. [swissprot;acc:p23396] Subtracted 241.612 265.119 23.507
fad synthetase. [refseq;acc:nm_025207] Divided 241.373 267.352 1.10763
271 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Subtracted 243.072 266.559 23.487
272 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Divided 241.373 267.352 1.10763
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Subtracted 242.83 266.248 23.418
273 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Divided 241.373 267.352 1.10763
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Subtracted 243.208 266.617 23.409
274 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] 242.744 266.07 23.326
nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Divided 241.373 267.352 1.10763
275 40s ribosomal protein s5. [swissprot;acc:p46782] Subtracted 242.473 265.756 23.283
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Divided 241.373 267.352 1.10763
276 60s ribosomal protein l32. [swissprot;acc:p02433] 241.13 266.969 1.10716
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] Subtracted 258.437 235.183 23.254
277 40s ribosomal protein s29. [swissprot;acc:p30054] Divided 241.849 267.642 1.10665
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Subtracted 239.277 262.434 23.157
278 40s ribosomal protein s11. [swissprot;acc:p04643] Divided 241.399 267.088 1.10642
myelin gene expression factor 2. [refseq;acc:nm_016132] Subtracted 235.383 258.476 23.093
279 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] Divided 252.644 228.42 1.10605
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Subtracted 242.66 265.715 23.055
280 metastasis-associated protein mta1. [swissprot;acc:q13330] Divided 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
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] 252.39 228.297 1.10553
nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438] Subtracted 242.159 265.104 22.945
283 60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7] 242.37 265.255 22.885
60s ribosomal protein l11. [swissprot;acc:p39026] Divided 241.828 267.346 1.10552
284 crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945] 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
285 dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] 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
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] Divided 224.633 203.251 1.1052
287 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] 240.758 266.079 1.10517
splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Subtracted 225.217 202.459 22.758

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/