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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Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2858 to 2907 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
358 microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Measured Divided 5061.11 5950.22 1.17567
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208] Rooted Subtracted 51.6736 58.4422 6.7686
ras-related protein rab-37. [swissprot;acc:q96ax2] Ranked 240.287 260.193 19.906
ribosomal protein l10-like protein. [refseq;acc:nm_080746] Divided 243.12 266.662 1.09683
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Measured Subtracted 4977.8 5966.14 988.34
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, alpha isoform (pp2a, subunit b, b-alpha isoform) (pp2a, subunit b, b55-alpha isoform) (pp2a, subunit b, pr55-alpha isoform) (pp2a, subunit b, r2-alpha isoform). [swissprot;acc:q00007] Squared Divided 9811.73 7908.13 1.24071
serine/threonine-protein kinase nek2 (ec 2.7.1.37) (nima-related protein kinase 2) (nima-like protein kinase 1) (hspk 21). [swissprot;acc:p51955] Rooted 61.2684 67.755 1.10587
359 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Squared Subtracted 34129.4 40434.2 6304.8
60s ribosomal protein l4 (l1). [swissprot;acc:p36578] Ranked Divided 239.277 262.434 1.09678
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526] Measured 12798.9 10887.2 1.17559
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Subtracted 1920.75 2907.43 986.68
pescadillo homolog 1. [swissprot;acc:o00541] Rooted Divided 49.2488 54.4603 1.10582
ras-related protein rab-26. [swissprot;acc:q9ulw5] Ranked Subtracted 240.287 260.193 19.906
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Squared Divided 9812.34 7908.87 1.24068
squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146] Rooted Subtracted 57.6823 64.4212 6.7389
360 atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 46.901 53.624 6.723
dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387] Ranked 240.287 260.193 19.906
g2/mitotic-specific cyclin b2. [swissprot;acc:o95067] Measured Divided 12796.8 10886 1.17553
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Rooted 49.3771 54.5905 1.10558
protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] Ranked 243.072 266.559 1.09663
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Squared 9814.47 7911.48 1.24054
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Measured Subtracted 4590.18 5575.52 985.34
vav-2 protein. [swissprot;acc:p52735] Squared 31377.3 37670.1 6292.8
361 40s ribosomal protein s4, y isoform 2. [swissprot;acc:q8td47] Rooted Divided 50.7801 45.9472 1.10518
calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] Subtracted 46.8525 53.5324 6.6799
cbl e3 ubiquitin protein ligase (ec 6.3.2.-) (signal transduction protein cbl) (proto-oncogene c-cbl). [swissprot;acc:p22681] Measured 6875.08 7858.38 983.3
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941] Divided 12787.6 10880.5 1.17528
katanin p60 subunit a 1. [refseq;acc:nm_007044] Ranked Subtracted 232.431 252.238 19.807
mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] Divided 242.83 266.248 1.09644
splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] Squared 70694.1 56989.9 1.24047
translationally controlled tumor protein (tctp) (p23) (histamine- releasing factor) (hrf). [swissprot;acc:p13693] Subtracted 42363.8 36083.8 6280
362 40s ribosomal protein s4, x isoform (single copy abundant mrna protein) (scr10). [swissprot;acc:p12750] Rooted Divided 50.7803 45.9477 1.10518
apical-like protein (apxl protein). [swissprot;acc:q13796] Ranked 231.492 211.136 1.09641
calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] Rooted Subtracted 46.8525 53.5316 6.6791
g2/mitotic-specific cyclin b1. [swissprot;acc:p14635] Measured Divided 12786.6 10879.9 1.17525
katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] Ranked Subtracted 232.382 252.166 19.784
nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594] Squared 34071.5 40336.5 6265
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Measured 4981.52 5964.58 983.06
transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545] Squared Divided 57808.9 46630.3 1.23973
363 alpha-nac protein. [sptrembl;acc:q9h009] Subtracted 34069.4 40333 6263.6
block of proliferation 1. [swissprot;acc:q14137] Rooted Divided 49.4884 54.6735 1.10477
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493] Measured 12780.7 10876.4 1.17509
set domain and mariner transposase fusion gene. [refseq;acc:nm_006515] Ranked Subtracted 233.539 253.197 19.658
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Divided 231.481 211.131 1.09639
signal transduction protein cbl-b (sh3-binding protein cbl-b). [swissprot;acc:q13191] Measured Subtracted 6856.71 7838.3 981.59
tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [refseq;acc:nm_024885] Squared Divided 57579.2 46497.2 1.23834
u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8] Rooted Subtracted 56.48 63.119 6.639
364 cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257] Ranked 233.539 253.197 19.658
dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Rooted Divided 50.0785 55.3215 1.1047
dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] Ranked 243.208 266.617 1.09625

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/