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 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
438 nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556] Subtracted 6739.85 7644.63 904.78
swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497] Divided 6252.58 7192.88 1.15039
439 programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]
similar to expressed sequence aa415817. [sptrembl;acc:q8n4q9] Subtracted 6739.85 7644.63 904.78
440 calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632] Divided 6251.91 7192.08 1.15038
homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356] Subtracted 6740.5 7644.76 904.26
441 grancalcin. [swissprot;acc:p28676] Divided 6251.96 7192.13 1.15038
u6 snrna-associated sm-like protein lsm7. [swissprot;acc:q9uk45] Subtracted 4598.21 5500.48 902.27
442 ptb domain adaptor protein ced-6; engulfment adapter protein. [refseq;acc:nm_016315] 5189 6088.47 899.47
sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626] Divided 6251.99 7192.17 1.15038
443 brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732] 6252.27 7192.51
calcyphosine. [swissprot;acc:q13938] Subtracted 5189 6088.47 899.47
444 crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848] Divided 3758.67 4322.87 1.15011
445 ad24 protein. [refseq;acc:nm_022451] 3753.71 4315.95 1.14978
guanine nucleotide-binding protein beta subunit 5 (transducin beta chain 5). [swissprot;acc:o14775] Subtracted 1857.32 958.237 899.083
446 enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] 4991.02 5885.09 894.07
nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Divided 3766.03 4329.37 1.14958
447 pescadillo homolog 1. [swissprot;acc:o00541] 3751.14 4310.89 1.14922
splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435] Subtracted 4991.02 5885.09 894.07
448 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 4987.58 4094.57 893.01
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385] Divided 6259.3 7190.91 1.14884
449 imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Subtracted 5061.11 5950.22 889.11
wd-repeat protein 12 (ytm1 homolog). [swissprot;acc:q9gzl7] Divided 3761.59 4319.69 1.14837
450 l-myc-1 proto-oncogene protein. [swissprot;acc:p12524] 4889.21 5610.52 1.14753
microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378] Subtracted 5061.11 5950.22 889.11
451 n-myc proto-oncogene protein. [swissprot;acc:p04198] Divided 4889.71 5610.69 1.14745
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] Subtracted 398.5 1281.5 883
452 tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]
zinc finger-like protein 9. [refseq;acc:nm_033414] Divided 3760.8 4315.06 1.14738
453 dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] Subtracted 398.5 1281.5 883
membrane-associated transporter protein (aim-1 protein) (melanoma antigen aim1). [swissprot;acc:q9umx9] Divided 3760.8 4315.06 1.14738
454 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Subtracted 398.5 1281.5 883
guanine nucleotide-binding protein-like 1 (gtp-binding protein hsr1). [swissprot;acc:p36915] Divided 3760.8 4315.06 1.14738
455 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Subtracted 398.5 1281.5 883
ga binding protein alpha chain (gabp-alpha subunit) (transcription factor e4tf1-60) (nuclear respiratory factor-2 subunit alpha). [swissprot;acc:q06546] Divided 4890.51 5610.95 1.14731
456 ga binding protein beta-2 chain (gabp-beta-2 subunit) (transcription factor e4tf1-47) (gapbp-2) (nuclear respiratory factor-2 subunit gamma). [swissprot;acc:q06545]
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted 398.5 1281.5 883
457 nadh-ubiquinone oxidoreductase 23 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-23kd) (ci-23kd) (tyky subunit). [swissprot;acc:o00217] Divided 4890.51 5610.95 1.14731
u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0] Subtracted 4620.76 5501.94 881.18
458 elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Divided 4890.55 5610.96 1.14731
grb2-related adaptor protein. [swissprot;acc:q13588] Subtracted 5986.65 6865.68 879.03
459 myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Divided 4892.16 5611.48 1.14704
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Subtracted 5082.66 5959.99 877.33
460 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 1 (transducin beta chain 1). [swissprot;acc:p04901] 1931.34 1057.39 873.95
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Divided 3790.11 4346.98 1.14693
461 grb2-related adaptor protein. [swissprot;acc:q13588] 5986.65 6865.68 1.14683
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 2353.63 3225.65 872.02
462 ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] Divided 11383.2 9926.61 1.14674
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted 2353.63 3225.65 872.02

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/