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 Value Type description 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
Value Type
description
red
green
network_comparison
513 Squared transforming protein rhoc (h9). [swissprot;acc:p08134] 19987.6 23960.7 1.19878
Rooted 60s ribosomal protein l4 (l1). [swissprot;acc:p36578] 51.5881 47.3127 1.09036
514 Measured 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] 7477 8532.02 1.1411
Ranked segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [swissprot;acc:o14641] 218.613 204.382 1.06963
Squared thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] 19987.6 23960.7 1.19878
Rooted xpa-binding protein 2 (hcnp protein) (pp3898). [swissprot;acc:q9hcs7] 58.7805 64.0772 1.09011
515 Measured transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 3890.53 4439.07 1.14099
Ranked pescadillo homolog 1. [swissprot;acc:o00541] 251.297 234.941 1.06962
Squared 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325] 19987.6 23960.7 1.19878
Rooted u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [swissprot;acc:o15116] 56.3551 61.4322 1.09009
516 Measured n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] 4910.6 5600.61 1.14051
Ranked u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] 228.255 213.422 1.0695
Squared transforming protein rhoa (h12). [swissprot;acc:p06749] 19987.6 23960.7 1.19878
Rooted adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819] 50.7935 46.6042 1.08989
517 Measured galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] 4910.6 5600.61 1.14051
Ranked metaxin 2. [swissprot;acc:o75431] 219.537 234.793 1.06949
Squared splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 19263.3 23092.3 1.19877
Rooted eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 50.0578 54.5502 1.08974
518 Measured udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] 4910.6 5600.61 1.14051
Ranked nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] 250.858 234.563 1.06947
Squared proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] 11447.3 13719.2 1.19847
Rooted trinucleotide repeat containing 15. [refseq;acc:nm_015575] 50.0578 54.5502 1.08974
519 Measured glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] 9648.27 10994.9 1.13957
Ranked segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] 218.702 204.582 1.06902
Squared polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] 22387.1 26827.3 1.19834
Rooted septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] 114.309 124.527 1.08939
520 Measured endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] 9642.22 10986.4 1.13941
Ranked sqv-7-like protein (fragment). [sptrembl;acc:o95454] 214.754 229.565 1.06897
Squared paxillin. [swissprot;acc:p49023] 22387.1 26827.3 1.19834
Rooted breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] 61.1902 66.6503 1.08923
521 Measured u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] 5390.78 6142.07 1.13937
Ranked exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] 215.237 230.07 1.06891
Squared carboxypeptidase a5. [refseq;acc:nm_080385] 53174 44377.4 1.19822
Rooted 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] 61.1902 66.6503 1.08923
522 Measured glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] 9634.98 10976.2 1.1392
Ranked pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] 222.893 208.523 1.06891
Squared carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] 53174 44377.4 1.19822
Rooted septin 10 isoform 1. [refseq;acc:nm_144710] 113.733 123.871 1.08914
523 Measured aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] 10640.2 12117.8 1.13887
Ranked exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] 215.237 230.07 1.06891
Squared neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837] 53174 44377.4 1.19822
Rooted ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] 66.377 72.2842 1.08899
524 Measured aquaporin 5. [swissprot;acc:p55064] 10640 12117.6 1.13887
Ranked exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5] 215.237 230.07 1.06891
Squared aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154] 53174 44377.4 1.19822
Rooted brain protein 44. [swissprot;acc:o95563] 113.374 123.463 1.08899
525 Measured lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] 10639.8 12117.3 1.13887
Ranked exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4] 215.237 230.07 1.06891
Squared carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] 53174 44377.4 1.19822
Rooted septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] 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/