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.


Navigation/Query Panel:
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 24226 to 24275 of 29840 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
2527 60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1] Measured Subtracted 3730.53 3611.05 119.48
importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] Ranked 201.96 201.488 0.472
large proline-rich protein bat3 (hla-b-associated transcript 3) (g3). [swissprot;acc:p46379] Measured Divided 8695.15 8912.98 1.02505
sequestosome 1; ubiquitin-binding protein p62; phosphotyrosine independent ligand for the lck sh2 domain p62. [refseq;acc:nm_003900] Squared 32402.9 34188.4 1.0551
star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2] Rooted 62.4421 63.0512 1.00975
transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] Ranked 209.143 208.659 1.00232
tubulin gamma-2 chain (gamma-2 tubulin). [swissprot;acc:q9nrh3] Rooted Subtracted 66.145 66.7577 0.6127
2528 40s ribosomal protein s16. [swissprot;acc:p17008] Measured 3730.53 3611.05 119.48
alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] Rooted Divided 62.4421 63.0512 1.00975
forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] Squared Subtracted 5313 6389.9 1076.9
keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4] Rooted 62.4421 63.0515 0.6094
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [swissprot;acc:p22307] Squared Divided 32402.9 34188.4 1.0551
reticulon 4 (neurite outgrowth inhibitor) (nogo protein) (foocen) (neuroendocrine-specific protein) (nsp) (neuroendocrine specific protein c homolog) (rtn-x) (reticulon 5) (my043 protein). [swissprot;acc:q9nqc3] Measured 6205.14 6359.44 1.02487
scribble. [refseq;acc:nm_015356] Ranked 221.782 222.291 1.0023
transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907] Subtracted 201.96 201.488 0.472
2529 60s ribosomal protein l11. [swissprot;acc:p39026] Squared 12200.6 13277 1076.4
60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429] Measured 3730.74 3611.45 119.29
keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184] Rooted 62.4421 63.0515 0.6094
lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214] Ranked Divided 221.776 222.283 1.00229
pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059] Rooted 62.4421 63.0512 1.00975
protein cgi-147. [swissprot;acc:q9y3e5] Measured 6436.43 6283 1.02442
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584] Squared 30390.4 32033.8 1.05408
transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] Ranked Subtracted 201.96 201.488 0.472
2530 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] Measured Divided 3880.5 3788.42 1.02431
60s ribosomal protein l15. [swissprot;acc:p39030] Subtracted 4888.72 5006.1 117.38
60s ribosomal protein l22 (epstein-barr virus small rna associated protein) (eber associated protein) (eap) (heparin binding protein hbp15). [swissprot;acc:p35268] Squared Divided 38544.3 36568.4 1.05403
chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] Ranked Subtracted 187.902 188.366 0.464
forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] Squared 5302.25 6378.24 1075.99
integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418] Rooted Divided 62.4421 63.0512 1.00975
keratin associated protein 1.5. [refseq;acc:nm_031957] Subtracted 63.0515 0.6094
proteasome subunit beta type 8 precursor (ec 3.4.25.1) (proteasome component c13) (macropain subunit c13) (multicatalytic endopeptidase complex subunit c13). [swissprot;acc:p28062] Ranked Divided 212.464 211.99 1.00224
2531 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 216.264 215.787 1.00221
forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] Squared Subtracted 5301.97 6377.93 1075.96
keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690] Rooted 62.4421 63.0515 0.6094
lim/homeobox protein lhx3. [swissprot;acc:q9ubr4] Measured 7571.73 7688.39 116.66
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780] Divided 6141.97 6291.08 1.02428
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404] Rooted 62.4421 63.0512 1.00975
sin3 associated polypeptide p30; sin3-associated polypeptide, 30kd. [refseq;acc:nm_003864] Squared 38544.3 36568.4 1.05403
vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] Ranked Subtracted 215.964 216.421 0.457
2532 54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233] Divided 190.405 190.812 1.00214
60s ribosomal protein l15. [swissprot;acc:p39030] Measured 4888.72 5006.1 1.02401
clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172] Squared 38544.3 36568.4 1.05403
gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] Ranked Subtracted 217.144 216.699 0.445
keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371] Rooted 62.4421 63.0515 0.6094
lim domain binding 2; lim binding domain 2; lim domain-binding factor-2. [refseq;acc:nm_001290] Measured 7572.69 7689.04 116.35
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] Squared 6585.44 7655.13 1069.69
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86] Rooted Divided 62.4421 63.0512 1.00975
2533 atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450] Squared 38544.3 36568.4 1.05403
dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6] Measured 3847.84 3759.28 1.02356
espin. [refseq;acc:nm_031475] Rooted 62.4421 63.0512 1.00975

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/