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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Rank Gene Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1775 to 1824 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
444 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
Rooted adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 50.4595 46.0415 1.09596
453 Measured membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] 3760.8 4315.06 1.14738
Ranked u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 224.161 207.972 1.07784
Squared serine/threonine protein phosphatase 6 (ec 3.1.3.16) (pp6). [swissprot;acc:o00743] 31620.5 38250.7 1.20968
Rooted surfeit locus protein 5. [swissprot;acc:q15528] 50.4595 46.0413 1.09596
454 Measured guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] 3760.8 4315.06 1.14738
Ranked 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
Squared sporulation-induced transcript 4-associated protein. [refseq;acc:nm_018312] 31620.5 38250.7 1.20968
Rooted gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] 50.4595 46.0412 1.09596
455 Measured ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] 4890.51 5610.95 1.14731
Ranked mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] 210.225 226.578 1.07779
Squared acetyl-coa carboxylase 1 (ec 6.4.1.2) (acc-alpha) [includes: biotin carboxylase (ec 6.3.4.14)]. [swissprot;acc:q13085] 31597.8 38216.9 1.20948
Rooted zinc finger protein 291. [swissprot;acc:q9by12] 50.4595 46.0413 1.09596
456 Measured ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545] 4890.51 5610.95 1.14731
Ranked atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] 210.225 226.578 1.07779
Squared nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4] 10933.6 13219.6 1.20908
Rooted peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933] 50.4595 46.0413 1.09596

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/