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 2980 to 3029 of 14920 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Value Type
Filtered
red
green
network_comparison
373 kynureninase (ec 3.7.1.3) (l-kynurenine hydrolase). [swissprot;acc:q16719] Measured 0 2713.5 2864.68 1.05571
mitogen-activated protein kinase kinase kinase 5 (ec 2.7.1.-) (mapk/erk kinase kinase 5) (mek kinase 5) (mekk 5) (apoptosis signal- regulating kinase 1) (ask-1). [swissprot;acc:q99683] Ranked 10598.2 11061.5 1.04371
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110] Measured 1 5066.99 5926.1 1.16955
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 0 30.3054 31.5389 1.0407
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Squared 215.107 192.635 1.11666
374 60s ribosomal protein l26. [swissprot;acc:q02877] Rooted 1 50.2549 45.5599 1.10305
adenine phosphoribosyltransferase (ec 2.4.2.7) (aprt). [swissprot;acc:p07741] Measured 0 2323.8 2452.23 1.05527
alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] Squared 2572.14 2869.96 1.11579
calcyphosine. [swissprot;acc:q13938] Ranked 9874.54 9478.1 1.04183
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted 30.2858 31.5117 1.04048
serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743] Measured 1 5066.93 5925.38 1.16942
spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6] Squared 45987 56777.1 1.23463
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Ranked 267.208 244.168 1.09436
375 45 kda calcium-binding protein precursor (cab45) (stromal cell-derived factor 4) (sdf-4). [swissprot;acc:q9brk5] Squared 45987 56777.1 1.23463
60s ribosomal protein l35. [swissprot;acc:p42766] Rooted 50.2545 45.5637 1.10295
dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802] Ranked 242.686 265.516 1.09407
estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061] Measured 0 2323.8 2452.23 1.05527
germ cell-less. [refseq;acc:nm_022471] Rooted 27.8491 26.7806 1.0399
importin 9. [refseq;acc:nm_018085] Squared 1062.18 952.74 1.11487
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Ranked 14247.6 13686.9 1.04097
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Measured 1 4700.42 5492.63 1.16854
376 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Rooted 0 32.3671 31.1453 1.03923
40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 1 50.2554 45.5688 1.10285
44050 protein. [refseq;acc:nm_178832] Measured 17385.9 14889.2 1.16769
galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470] Squared 46021.4 56813.2 1.2345
nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733] 0 1062.18 952.74 1.11487
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93] Ranked 1 257.017 234.945 1.09395
protein-tyrosine phosphatase, non-receptor type 1 (ec 3.1.3.48) (protein-tyrosine phosphatase 1b) (ptp-1b). [swissprot;acc:p18031] Measured 0 4912.01 4658.69 1.05438
ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930] Ranked 10284.9 10695.6 1.03993
377 60s acidic ribosomal protein p1. [swissprot;acc:p05386] Rooted 45.8794 47.6722 1.03908
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] Measured 884.254 931.405 1.05332
creatine kinase, ubiquitous mitochondrial precursor (ec 2.7.3.2) (u- mtck) (mia-ck) (acidic-type mitochondrial creatine kinase). [swissprot;acc:p12532] Squared 570.099 634.654 1.11323
dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602] Ranked 1 242.691 265.481 1.09391
integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106] 0 14512.3 13958.2 1.0397
mitochondrial ribosomal protein l2. [refseq;acc:nm_015950] Rooted 1 50.2554 45.5687 1.10285
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972] Measured 17385.9 14889.2 1.16769
ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926] Squared 33044.9 40781.4 1.23412
378 60s ribosomal protein l30. [swissprot;acc:p04645] Ranked 242.593 265.365 1.09387
actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571] Measured 0 703.068 739.623 1.05199
anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5] Rooted 74.2677 71.5378 1.03816
eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] Squared 1 15034.5 18552.2 1.23398
hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] Measured 12471.7 14561.7 1.16758
mitochondrial ribosomal protein l4 isoform a. [refseq;acc:nm_015956] Rooted 50.5816 45.8738 1.10263
neurocalcin delta. [swissprot;acc:p29554] Squared 0 4946.59 5466.65 1.10514
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0] Ranked 19713.5 18962.5 1.0396
379 26s proteasome non-atpase regulatory subunit 10 (26s proteasome regulatory subunit p28) (gankyrin). [swissprot;acc:o75832] 11228.4 10806 1.03909
adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 1 241.509 264.163 1.0938
aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763] Squared 33010.8 40732.2 1.23391
ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447] Measured 0 1927.62 1833.64 1.05125
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Rooted 1 59.5128 65.604 1.10235

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/