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 2051 to 2100 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
513 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Ranked 218.596 204.344 1.06975
transforming protein rhoc (h9). [swissprot;acc:p08134] Squared 19987.6 23960.7 1.19878
514 1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [swissprot;acc:q9nrz5] Measured 7477 8532.02 1.1411
segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] Ranked 218.613 204.382 1.06963
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] Squared 19987.6 23960.7 1.19878
xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] Rooted 58.7805 64.0772 1.09011
515 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] Squared 19987.6 23960.7 1.19878
pescadillo homolog 1. [swissprot;acc:o00541] Ranked 251.297 234.941 1.06962
transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] Measured 3890.53 4439.07 1.14099
u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] Rooted 56.3551 61.4322 1.09009
516 adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 50.7935 46.6042 1.08989
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Measured 4910.6 5600.61 1.14051
transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 19987.6 23960.7 1.19878
u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Ranked 228.255 213.422 1.0695
517 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] Rooted 50.0578 54.5502 1.08974
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Measured 4910.6 5600.61 1.14051
metaxin 2. [swissprot;acc:o75431] Ranked 219.537 234.793 1.06949
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Squared 19263.3 23092.3 1.19877
518 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Ranked 250.858 234.563 1.06947
proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Squared 11447.3 13719.2 1.19847
trinucleotide repeat containing 15. [refseq;acc:nm_015575] Rooted 50.0578 54.5502 1.08974
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Measured 4910.6 5600.61 1.14051
519 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 9648.27 10994.9 1.13957
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Squared 22387.1 26827.3 1.19834
segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Ranked 218.702 204.582 1.06902
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Rooted 114.309 124.527 1.08939
520 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 61.1902 66.6503 1.08923
endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Measured 9642.22 10986.4 1.13941
paxillin. [swissprot;acc:p49023] Squared 22387.1 26827.3 1.19834
sqv-7-like protein (fragment). [sptrembl;acc:o95454] Ranked 214.754 229.565 1.06897
521 carboxypeptidase a5. [refseq;acc:nm_080385] Squared 53174 44377.4 1.19822
cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253] Rooted 61.1902 66.6503 1.08923
exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Ranked 215.237 230.07 1.06891
u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Measured 5390.78 6142.07 1.13937
522 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Squared 53174 44377.4 1.19822
glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Measured 9634.98 10976.2 1.1392
pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Ranked 222.893 208.523 1.06891
septin 10 isoform 1. [refseq;acc:nm_144710] Rooted 113.733 123.871 1.08914
523 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Measured 10640.2 12117.8 1.13887
exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Ranked 215.237 230.07 1.06891
neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] Squared 53174 44377.4 1.19822
ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Rooted 66.377 72.2842 1.08899
524 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] Squared 53174 44377.4 1.19822
aquaporin 5. [swissprot;acc:p55064] Measured 10640 12117.6 1.13887
brain protein 44. [swissprot;acc:o95563] Rooted 113.374 123.463 1.08899
exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] Ranked 215.237 230.07 1.06891
525 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Squared 53174 44377.4 1.19822
exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] Ranked 215.237 230.07 1.06891
lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Measured 10639.8 12117.3 1.13887
septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Rooted 113.374 123.463 1.08899

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/