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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1758 to 1807 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
440 CAPNS1 Measured calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] 6251.91 7192.08 1.15038
DOK2 Rooted docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] 63.2134 69.352 1.09711
NDC80 Ranked highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] 231.802 249.983 1.07843
441 DOK1 Rooted docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] 63.2134 69.352 1.09711
GCA Measured grancalcin. [swissprot;acc:p28676] 6251.96 7192.13 1.15038
GRAP Ranked grb2-related adaptor protein. [swissprot;acc:q13588] 223.457 207.222 1.07835
TOP2B Squared dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] 26348.7 31924.3 1.21161
442 ANKS1B Ranked e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 207.55 1.0783
CENPJ 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
FRK Rooted tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] 63.2134 69.352 1.09711
SRI Measured sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] 6251.99 7192.17 1.15038
443 no value Rooted 60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025] 50.1766 45.7369 1.09707
ARID1B Measured brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 6252.27 7192.51 1.15038
MTIF2 Squared translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199] 26472.8 32067.7 1.21135
NAV2 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
444 no value Rooted 60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635] 50.1636 45.7275 1.09701
EBNA1BP2 Measured probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] 3758.67 4322.87 1.15011
NAV1 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
UBE2E1 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
445 NAV3 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
NOC3L Measured ad24 protein. [refseq;acc:nm_022451] 3753.71 4315.95 1.14978
RPL10L Rooted ribosomal protein l10-like protein. [refseq;acc:nm_080746] 50.1635 45.7274 1.09701
UBE2E4P Squared ubiquitin-conjugating enzyme e2e 3; ubiquitin carrier protein; ubiquitin-protein ligase. [refseq;acc:nm_006357] 58831 48584.2 1.21091
446 EIF4E 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
GNL3 Measured nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 3766.03 4329.37 1.14958
GRB2 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
SORBS1 Squared ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 29335.6 35515.5 1.21066
447 ADI1 sipl protein. [refseq;acc:nm_018269] 30155.1 36495 1.21024
BAIAP3 Rooted bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933] 54.9019 60.2111 1.0967
NEK2 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
PES1 Measured pescadillo homolog 1. [swissprot;acc:o00541] 3751.14 4310.89 1.14922
448 CAPN1 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
MACF1 Ranked microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] 228.468 246.338 1.07822
SEC61G Rooted protein transport protein sec61 gamma subunit. [swissprot;acc:p38384] 50.1671 45.7563 1.0964
SORBS1 Measured ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] 6259.3 7190.91 1.14884
449 CAPN2 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
DST 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
POLR2B 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
WDR12 Measured wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] 3761.59 4319.69 1.14837
450 ACACB 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
CMPK 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
MYCL1 Measured l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] 4889.21 5610.52 1.14753
SRP9 Ranked signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 235.94 218.837 1.07815
451 no value Squared small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 17543.3 21222.5 1.20972
MRPL17 Rooted mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061] 50.268 45.8663 1.09597
MYCN Measured n-myc proto-oncogene protein. [swissprot;acc:p04198] 4889.71 5610.69 1.14745
POLR3C Ranked polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 239.092 257.705 1.07785
452 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 207.972 1.07784
Rooted adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] 50.4595 46.0415 1.09596
SNRPF 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
- Hugo is the HGNC identifier if it exists
- 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/