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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Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 875 to 924 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
438 n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] High confidence 233.723 216.674 1.07869
rna polymerase ii elongation factor ell (eleven-nineteen lysine-rich leukemia protein). [swissprot;acc:p55199] Low confidence 198.572 205.504 1.03491
439 40s ribosomal protein s9. [swissprot;acc:p46781] High confidence 238.986 257.784 1.07866
beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Low confidence 194.237 187.689 1.03489
440 highly expressed in cancer, rich in leucine heptad repeats. [refseq;acc:nm_006101] High confidence 231.802 249.983 1.07843
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] Low confidence 203.045 196.204 1.03487
441 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584]
grb2-related adaptor protein. [swissprot;acc:q13588] High confidence 223.457 207.222 1.07835
442 e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140] 223.802 207.55 1.0783
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Low confidence 201.424 194.652 1.03479
443 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 201.418 194.664 1.0347
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] High confidence 223.79 207.539 1.0783
444 neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443] 223.801 207.549
u5 snrnp-associated 102 kda protein (u5-102 kda protein). [swissprot;acc:o94906] Low confidence 207.002 200.066 1.03467
445 neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [refseq;acc:nm_014903] High confidence 223.801 207.549 1.0783
serologically defined colon cancer antigen 16. [refseq;acc:nm_006649] Low confidence 206.703 199.782 1.03464
446 f16601_1, partial cds (fragment). [sptrembl;acc:o75274]
growth factor receptor-bound protein 2 (grb2 adapter protein) (sh2/sh3 adapter grb2) (ash protein). [swissprot;acc:p29354] High confidence 224.049 207.785 1.07827
447 gene amplified in squamous cell carcinoma 1. [refseq;acc:nm_015061] Low confidence 206.703 199.782 1.03464
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] High confidence 224.049 207.785 1.07827
448 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Low confidence 203.074 196.277 1.03463
microtubule-actin crosslinking factor 1, isoform 4. [swissprot;acc:q96pk2] High confidence 228.468 246.338 1.07822
449 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
cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928] Low confidence 203.077 196.283 1.03461
450 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 207.786 200.839 1.03459
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 235.94 218.837 1.07815
451 polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 239.092 257.705 1.07785
similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Low confidence 210.594 203.561 1.03455
452 ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] High confidence 224.161 207.972 1.07784
nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Low confidence 202.01 195.266 1.03454
453 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] 210.727 203.693 1.03453
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] High confidence 224.161 207.972 1.07784
454 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] Low confidence 210.252 203.24 1.0345
455 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] High confidence 210.225 226.578 1.07779
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Low confidence 210.251 203.241 1.03449
456 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] High confidence 210.225 226.578 1.07779
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Low confidence 210.251 203.241 1.03449
457 ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] High confidence 210.225 226.578 1.07779
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Low confidence 210.251 203.241 1.03449
458 adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567] 206.948 200.058 1.03444
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] High confidence 235.922 218.925 1.07764
459 bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] 233.529 216.737 1.07748
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Low confidence 207.797 214.954 1.03444
460 proactivator polypeptide precursor [contains: saposin a (protein a); saposin b (sphingolipid activator protein 1) (sap-1) (cerebroside sulfate activator) (csact) (dispersin) (sulfatide/gm1 activator); saposin c (co-beta-glucosidase) (a1 activator) (glucosylceramidase activator) (sphingolipid activator protein 2) (sap-2); saposin d (protein c) (component c)]. [swissprot;acc:p07602] 209.188 202.243 1.03434
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] High confidence 223.648 207.62 1.0772
461 huntingtin interacting protein c. [refseq;acc:nm_012272] Low confidence 201.429 194.776 1.03416
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] High confidence 223.648 207.62 1.0772
462 large neutral amino acids transporter small subunit 1 (l-type amino acid transporter 1) (4f2 light chain) (4f2 lc) (4f2lc) (cd98 light chain) (integral membrane protein e16) (hlat1). [swissprot;acc:q01650] Low confidence 201.466 194.819 1.03412
mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] High confidence 254.434 236.224 1.07709

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/