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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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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2508 to 2557 of 3228 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
red
green
network_comparison
2508 CEECAM1 cerebral cell adhesion molecule. [refseq;acc:nm_016174] 194.349 193.871 1.00247
2509 CBX3 chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185] 187.902 188.366
2510 GRPEL2 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] 234.384 234.948 1.00241
2511 GRPEL1 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]
2512 SMARCD2 swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]
2513 SMARCD3 swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]
2514 SMARCD1 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]
2515 DFFB dna fragmentation factor 40 kda subunit (ec 3.-.-.-) (dff-40) (caspase-activated deoxyribonuclease) (caspase-activated dnase) (cad) (caspase-activated nuclease) (cpan). [swissprot;acc:o76075] 215.835 216.341 1.00234
2516 ADAMTS9 adamts-9 precursor (ec 3.4.24.-) (a disintegrin and metalloproteinase with thrombospondin motifs 9) (adam-ts 9) (adam-ts9). [swissprot;acc:q9p2n4]
2517 DFFA dna fragmentation factor alpha subunit (dna fragmentation factor 45 kda subunit) (dff-45) (inhibitor of cad) (icad). [swissprot;acc:o00273]
2518 ANK3 ankyrin 3 (ank-3) (ankyrin g). [swissprot;acc:q12955]
2519 ANK2 ankyrin 2 (brain ankyrin) (ankyrin b) (ankyrin, nonerythroid). [swissprot;acc:q01484]
2520 ARL3 adp-ribosylation factor-like protein 3. [swissprot;acc:p36405]
2521 no value nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7] 201.96 201.488
2522 UNC119 unc-119 protein homolog (retinal protein 4) (hrg4). [swissprot;acc:q13432] 215.835 216.341
2523 KPNB1 importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974] 201.96 201.488
2524 TBL1X transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]
2525 PSMD8 26s proteasome non-atpase regulatory subunit 8 (26s proteasome regulatory subunit s14) (p31). [swissprot;acc:p48556] 215.835 216.341
2526 TBL1Y transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87] 201.96 201.488
2527 TKTL1 transketolase-like 1 (ec 2.2.1.1) (transketolase 2) (tk 2) (transketolase related protein). [swissprot;acc:p51854] 209.143 208.659 1.00232
2528 SCRIB scribble. [refseq;acc:nm_015356] 221.782 222.291 1.0023
2529 LRRC1 lap (leucine-rich repeats and pdz) and no pdz protein. [refseq;acc:nm_018214] 221.776 222.283 1.00229
2530 no value 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] 212.464 211.99 1.00224
2531 APEX2 apurinic/apyrimidinic endonuclease 2; apurinic/apyrimidinic endonuclease-like 2; apex nuclease-like 2. [refseq;acc:nm_014481] 216.264 215.787 1.00221
2532 NONO 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] 190.405 190.812 1.00214
2533 PSPC1 paraspeckle protein 1. [refseq;acc:nm_018282] 190.417 190.824
2534 GPD2 glycerol-3-phosphate dehydrogenase, mitochondrial precursor (ec 1.1.99.5) (gpd-m) (gpdh-m). [swissprot;acc:p43304] 208 207.555
2535 CBX1 chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197] 188.228 188.63
2536 GGPS1 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] 236.51 236.008 1.00213
2537 VPS45 vacuolar protein sorting-associated protein 45 (h-vps45) (hlvps45). [swissprot;acc:q9nrw7] 215.964 216.421 1.00212
2538 SFPQ splicing factor, proline-and glutamine-rich (polypyrimidine tract- binding protein-associated splicing factor) (ptb-associated splicing factor) (psf) (dna-binding p52/p100 complex, 100 kda subunit). [swissprot;acc:p23246] 190.765 191.163 1.00209
2539 C21orf66 gc-rich sequence dna-binding factor homolog. [swissprot;acc:q9y5b6] 217.144 216.699 1.00205
2540 TLR2 toll-like receptor 2 precursor (toll/interleukin 1 receptor-like protein 4). [swissprot;acc:o60603]
2541 DARS aspartyl-trna synthetase (ec 6.1.1.12) (aspartate--trna ligase) (asprs). [swissprot;acc:p14868] 194.505 194.902 1.00204
2542 ING4 p29ing4; candidate tumor suppressor p33 ing1 homolog. [refseq;acc:nm_016162] 218.068 217.633 1.002
2543 BRPF1 tubulin tyrosine ligase-like protein hottl (hqp0207). [swissprot;acc:q9y4r7] 224.726 225.164 1.00195
2544 AMT aminomethyltransferase, mitochondrial precursor (ec 2.1.2.10) (glycine cleavage system t protein) (gcvt). [swissprot;acc:p48728] 212.67 212.262 1.00192
2545 no value proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065] 213.494 213.088 1.00191
2546 TAF9B tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] 197.138 197.507 1.00187
2547 no value glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410] 206.894 206.51 1.00186
2548 glycerol kinase, testis specific 1 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14409] 206.899 206.516 1.00185
2549 glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189] 206.902 206.519
2550 EPN2 epsin 2 isoform b; eps15 binding protein. [refseq;acc:nm_014964] 217.587 217.988 1.00184
2551 FBP2 fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757] 209.766 210.148 1.00182
2552 CDY1B testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8] 193.12 193.467 1.0018
2553 CDYL chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]
2554 CDY2B testis-specific chromodomain protein y protein 2. [swissprot;acc:q9y6f7]
2555 MAT2A s-adenosylmethionine synthetase gamma form (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-ii). [swissprot;acc:p31153] 212.953 212.572 1.00179
2556 CDYL2 chromodomain y-like protein 2. [refseq;acc:nm_152342] 193.119 193.46 1.00177
2557 EEF2 elongation factor 2 (ef-2). [swissprot;acc:p13639] 222.658 223.047 1.00175

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/