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.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1801 to 1850 of 16578 in total
Value Type  : Ranked
Filtered  : 1
Rank
Hugo
description
Network Comparison Type
Interaction Map
red
green
network_comparison
451 CYP4B1 cytochrome p450 4b1 (ec 1.14.14.1) (cypivb1) (p450-hp). [swissprot;acc:p13584] Subtracted Low confidence 203.045 196.204 6.841
LIMCH1 similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2] Divided 210.594 203.561 1.03455
NAV2 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] Subtracted High confidence 223.79 207.539 16.251
POLR3C polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] Divided 239.092 257.705 1.07785
452 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] 224.161 207.972 1.07784
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Subtracted 221.522 205.286 16.236
PRPF19 nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502] Divided Low confidence 202.01 195.266 1.03454
SNRPD2 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Subtracted 201.134 194.302 6.832
453 C19orf29 ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4] Divided 210.727 203.693 1.03453
HS3ST6 c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5] Subtracted 207.812 200.994 6.818
PXN paxillin. [swissprot;acc:p49023] High confidence 221.522 205.286 16.236
SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] Divided 224.161 207.972 1.07784
454 no value 40s ribosomal protein s26. [swissprot;acc:p02383] 210.224 226.578 1.07779
CACNG4 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
GRAP grb2-related adaptor protein. [swissprot;acc:q13588] Subtracted High confidence 223.457 207.222 16.235
HS3ST3A1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042] Low confidence 207.812 200.994 6.818
455 no value ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36] High confidence 224.161 207.972 16.189
CACNG2 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Divided Low confidence 210.251 203.241 1.03449
HS3ST3B1 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041] Subtracted 207.812 200.994 6.818
TIMM22 mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Divided High confidence 210.225 226.578 1.07779
456 ATPAF2 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]
CACNG8 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
HS3ST2 heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043] Subtracted 207.812 200.994 6.818
SNRPA1 u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] High confidence 224.161 207.972 16.189
457 CACNG3 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Divided Low confidence 210.251 203.241 1.03449
DCPS mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026] Subtracted 207.812 200.994 6.818
FNBP1 ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6] High confidence 210.578 226.764 16.186
UQCRB ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Divided 210.225 226.578 1.07779
458 AP1B1 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] Low confidence 206.948 200.058 1.03444
CYP4A22 dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5] Subtracted 203.074 196.277 6.797
DDX18 atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1] High confidence 251.653 235.506 16.147
SRP9 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] Divided 235.922 218.925 1.07764
459 BAG3 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
CYP4A11 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] Subtracted Low confidence 203.077 196.283 6.794
GNG10 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151] Divided 207.797 214.954 1.03444
RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Subtracted High confidence 250.538 234.401 16.137
460 no value 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] Divided Low confidence 209.188 202.243 1.03434
RBM39 rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498] Subtracted 208.29 201.499 6.791
RPS6KC1 ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424] High confidence 186.52 170.42 16.1
SF3A2 splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Divided 223.648 207.62 1.0772
461 no value ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] Subtracted 186.52 170.42 16.1
GTF3A transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Low confidence 193.291 186.506 6.785
KLF5 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] Divided High confidence 223.648 207.62 1.0772
PRPF40B huntingtin interacting protein c. [refseq;acc:nm_012272] Low confidence 201.429 194.776 1.03416
462 no value formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Subtracted 201.424 194.652 6.772
MKI67IP mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390] Divided High confidence 254.434 236.224 1.07709
POLR2H dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] Subtracted 236.662 252.708 16.046
SLC7A5 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] Divided Low confidence 201.466 194.819 1.03412
463 EXOC1 exocyst complex component sec3 (bm-012). [swissprot;acc:q9nv70] Subtracted 209.111 202.34 6.771
POLR3F dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] Divided High confidence 238.921 257.327 1.07704

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/