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 2908 to 2957 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
364 dok-like protein. [refseq;acc:nm_024872] Measured Subtracted 6102.59 7081.46 978.87
ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] Divided 5189 6088.47 1.17334
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Rooted Subtracted 60.594 67.2244 6.6304
sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] Squared Divided 17957.2 22234.1 1.23817
small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173] Subtracted 34068.1 40330.8 6262.7
365 60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6] Ranked Divided 242.744 266.07 1.09609
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Squared 17965.8 22243 1.23807
calcyphosine. [swissprot;acc:q13938] Measured 5189 6088.47 1.17334
di-ras2. [refseq;acc:nm_017594] Squared Subtracted 34068 40330.7 6262.7
docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496] Measured 6102.59 7081.46 978.87
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Ranked 233.539 253.197 19.658
proliferating-cell nucleolar antigen p120 (proliferation-associated nucleolar protein p120). [swissprot;acc:p46087] Rooted Divided 49.7541 54.9425 1.10428
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Subtracted 63.0715 56.4506 6.6209
366 40s ribosomal protein s15a. [swissprot;acc:p39027] Divided 50.5463 45.7763 1.1042
40s ribosomal protein s5. [swissprot;acc:p46782] Ranked 242.473 265.756 1.09602
apical-like protein (apxl protein). [swissprot;acc:q13796] Rooted Subtracted 60.6697 67.2802 6.6105
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6] Squared Divided 62783.5 50784.1 1.23628
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155] Ranked Subtracted 233.539 253.197 19.658
crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0] Measured Divided 5189 6088.47 1.17334
docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704] Subtracted 6102.59 7081.46 978.87
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Squared 29101.9 35347 6245.1
367 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] Rooted Divided 49.0882 54.2027 1.10419
basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414] Squared 62757.7 50767.8 1.23617
dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] Ranked Subtracted 218.827 238.407 19.58
dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Measured Divided 4024.4 4719.35 1.17268
heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272] Ranked 234.146 256.627 1.09601
programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340] Squared Subtracted 29101.9 35347 6245.1
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Rooted 60.6732 67.2827 6.6095
tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685] Measured 6102.59 7081.46 978.87
368 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] Squared 29098.8 35342.6 6243.8
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Ranked 218.827 238.407 19.58
dr1-associated protein 1; negative cofactor 2 alpha; dr1-associated corepressor. [refseq;acc:nm_006442] Squared Divided 51805.2 41916.4 1.23592
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Rooted Subtracted 63.0663 56.4667 6.5996
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Divided 49.5225 54.6817 1.10418
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Measured 5082.66 5959.99 1.17261
putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361] Subtracted 7756.51 8731.76 975.25
trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606] Ranked Divided 242.66 265.715 1.09501
369 60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815] 242.159 265.104 1.09475
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701] Measured 3583.56 4194.95 1.17061
dna-directed rna polymerase ii 23 kda polypeptide (ec 2.7.7.6) (rpb25) (xap4) (rpb5) (rpabc1). [swissprot;acc:p19388] Ranked Subtracted 239.977 259.525 19.548
galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182] Squared Divided 45960.8 56749.6 1.23474
methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582] Rooted 49.7435 45.0586 1.10397
nucleoside diphosphate kinase a (ec 2.7.4.6) (ndk a) (ndp kinase a) (tumor metastatic process-associated protein) (metastasis inhibition factor nm23) (nm23-h1). [swissprot;acc:p15531] Measured Subtracted 7755.69 8730.74 975.05
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Rooted 63.0663 56.4667 6.5996
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Squared 29096 35338.7 6242.7
370 grancalcin. [swissprot;acc:p28676] 29095.7 35338.3 6242.6
grb2-related adaptor protein. [swissprot;acc:q13588] Rooted 61.4282 68.0107 6.5825
lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Measured Divided 4108.15 4808.93 1.17058
methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579] Rooted 49.7435 45.0586 1.10397
muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] Ranked Subtracted 218.818 238.358 19.54

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/