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 Value Type Gene description Network Comparison Type Filtered Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 1758 to 1807 of 12912 in total
Network Comparison Type  : Divided
Filtered  : 1
Interaction Map  : High confidence
Rank
Value Type
description
red
green
network_comparison
440 Ranked highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 231.802 249.983 1.07843
Squared dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] 26348.4 31925.8 1.21168
Rooted docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 63.2134 69.352 1.09711
441 Measured grancalcin. [swissprot;acc:p28676] 6251.96 7192.13 1.15038
Ranked grb2-related adaptor protein. [swissprot;acc:q13588] 223.457 207.222 1.07835
Squared dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 26348.7 31924.3 1.21161
Rooted docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 63.2134 69.352 1.09711
442 Measured sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 6251.99 7192.17 1.15038
Ranked e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 207.55 1.0783
Squared centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451] 51286.6 42334.5 1.21146
Rooted tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 63.2134 69.352 1.09711
443 Measured brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 6252.27 7192.51 1.15038
Ranked neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117] 223.79 207.539 1.0783
Squared translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] 26472.8 32067.7 1.21135
Rooted 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 50.1766 45.7369 1.09707
444 Measured probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 3758.67 4322.87 1.15011
Ranked neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 223.801 207.549 1.0783
Squared ubiquitin-conjugating enzyme e2 e1 (ec 6.3.2.19) (ubiquitin-protein ligase e1) (ubiquitin carrier protein e1) (ubch6). [swissprot;acc:p51965] 58831 48584.2 1.21091
Rooted 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 50.1636 45.7275 1.09701
445 Measured ad24 protein. [refseq;acc:nm_022451] 3753.71 4315.95 1.14978
Ranked neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] 223.801 207.549 1.0783
Squared ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] 58831 48584.2 1.21091
Rooted ribosomal protein l10-like protein. [refseq;acc:nm_080746] 50.1635 45.7274 1.09701
446 Measured nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 3766.03 4329.37 1.14958
Ranked growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] 224.049 207.785 1.07827
Squared ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 29335.6 35515.5 1.21066
Rooted eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730] 54.9019 60.2111 1.0967
447 Measured pescadillo homolog 1. [swissprot;acc:o00541] 3751.14 4310.89 1.14922
Ranked 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] 224.049 207.785 1.07827
Squared sipl protein. [refseq;acc:nm_018269] 30155.1 36495 1.21024
Rooted bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 54.9019 60.2111 1.0967
448 Measured ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 6259.3 7190.91 1.14884
Ranked microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 228.468 246.338 1.07822
Squared calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 20350.3 16816.1 1.21017
Rooted protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] 50.1671 45.7563 1.0964
449 Measured wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 3761.59 4319.69 1.14837
Ranked bullous pemphigoid antigen 1 isoforms 1/2/3/4/5/8 (230 kda bullous pemphigoid antigen) (bpa) (hemidesmosomal plaque protein) (dystonia musculorum protein) (fragment). [swissprot;acc:q03001] 228.463 246.33 1.07821
Squared 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] 20348.5 16817.2 1.20998
Rooted dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876] 50.162 45.7659 1.09606
450 Measured l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] 4889.21 5610.52 1.14753
Ranked signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.94 218.837 1.07815
Squared acetyl-coa carboxylase 2 (ec 6.4.1.2) (acc-beta) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:o00763] 31646.1 38288.7 1.2099
Rooted ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] 50.4595 46.0411 1.09597
451 Measured n-myc proto-oncogene protein. [swissprot;acc:p04198] 4889.71 5610.69 1.14745
Ranked polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 239.092 257.705 1.07785
Squared small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 17543.3 21222.5 1.20972
Rooted mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] 50.268 45.8663 1.09597
452 Measured zinc finger-like protein 9. [refseq;acc:nm_033414] 3760.8 4315.06 1.14738
Ranked ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 207.972 1.07784
Squared small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 17543.3 21222.5 1.20972

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/