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 900 to 949 of 8289 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
450 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
463 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 238.921 257.327 1.07704
paired mesoderm homeobox protein 1 (prx-1) (paired related homeobox protein 1) (homeobox protein phox1). [swissprot;acc:p54821] Low confidence 194.41 201.036 1.03408
464 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] High confidence 210.578 226.764 1.07686
rna polymerase ii elongation factor ell2. [swissprot;acc:o00472] Low confidence 198.618 205.369 1.03399
465 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] 207.812 200.994 1.03392
neuronal acetylcholine receptor protein, alpha-7 chain precursor. [swissprot;acc:p36544] High confidence 248.152 267.226 1.07686
466 adenylate cyclase, type vi (ec 4.6.1.1) (atp pyrophosphate-lyase) (ca(2+)-inhibitable adenylyl cyclase). [swissprot;acc:o43306]
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Low confidence 207.812 200.994 1.03392
467 adenylate cyclase, type v (ec 4.6.1.1) (atp pyrophosphate-lyase) (adenylyl cyclase) (fragment). [swissprot;acc:o95622] High confidence 248.152 267.226 1.07686
heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Low confidence 207.812 200.994 1.03392
468 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]
leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66] High confidence 248.152 267.226 1.07686
469 fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]
mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Low confidence 207.812 200.994 1.03392
470 leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71] High confidence 248.152 267.226 1.07686
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Low confidence 198.464 191.96 1.03388
471 laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047] High confidence 248.152 267.226 1.07686
rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Low confidence 208.29 201.499 1.0337
472 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 201.847 195.283 1.03361
thymic stromal co-transporter. [refseq;acc:nm_033051] High confidence 248.152 267.226 1.07686
473 exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] Low confidence 209.111 202.34 1.03346
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629] High confidence 225.661 209.651 1.07637
474 potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389] 226.789 210.818 1.07576
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] Low confidence 171.213 165.68 1.0334
475 fucosidase, alpha-l- 2, plasma. [refseq;acc:nm_032020] 202.311 195.778 1.03337

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/