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 Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 2063 to 2112 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
description
Value Type
red
green
network_comparison
516 LSM8 u6 snrna-associated sm-like protein lsm8. [swissprot;acc:o95777] Ranked 228.255 213.422 1.0695
RHOA transforming protein rhoa (h12). [swissprot;acc:p06749] Squared 19987.6 23960.7 1.19878
517 no value 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
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
EIF3I 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
MTX2 metaxin 2. [swissprot;acc:o75431] Ranked 219.537 234.793 1.06949
518 no value trinucleotide repeat containing 15. [refseq;acc:nm_015575] Rooted 50.0578 54.5502 1.08974
GALE udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Measured 4910.6 5600.61 1.14051
GNL3 nucleostemin; putative nucleotide binding protein, estradiol-induced. [refseq;acc:nm_014366] Ranked 250.858 234.563 1.06947
PROSC proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903] Squared 11447.3 13719.2 1.19847
519 DVL3 segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997] Ranked 218.702 204.582 1.06902
GYS1 glycogen [starch] synthase, muscle (ec 2.4.1.11). [swissprot;acc:p13807] Measured 9648.27 10994.9 1.13957
POLI polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195] Squared 22387.1 26827.3 1.19834
SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Rooted 114.309 124.527 1.08939
520 no value endo-beta-n-acetylglucosaminidase. [refseq;acc:nm_022759] Measured 9642.22 10986.4 1.13941
BCAS2 breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872] Rooted 61.1902 66.6503 1.08923
PXN paxillin. [swissprot;acc:p49023] Squared 22387.1 26827.3 1.19834
SLC35D2 sqv-7-like protein (fragment). [sptrembl;acc:o95454] Ranked 214.754 229.565 1.06897
521 CDC5L 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
CPA5 carboxypeptidase a5. [refseq;acc:nm_080385] Squared 53174 44377.4 1.19822
EXOSC4 exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3] Ranked 215.237 230.07 1.06891
PRPF3 u4/u6-associated rna splicing factor. [refseq;acc:nm_004698] Measured 5390.78 6142.07 1.13937
522 CPB1 carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086] Squared 53174 44377.4 1.19822
GYS2 glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840] Measured 9634.98 10976.2 1.1392
PLRG1 pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669] Ranked 222.893 208.523 1.06891
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Rooted 113.733 123.871 1.08914
523 AQP4 aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087] Measured 10640.2 12117.8 1.13887
EXOSC2 exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868] Ranked 215.237 230.07 1.06891
RRM1 ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921] Rooted 66.377 72.2842 1.08899
SLC3A1 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
524 ACY1 aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]
AQP5 aquaporin 5. [swissprot;acc:p55064] Measured 10640 12117.6 1.13887
BRP44 brain protein 44. [swissprot;acc:o95563] Rooted 113.374 123.463 1.08899
EXOSC3 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 CPA1 carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085] Squared 53174 44377.4 1.19822
EXOSC5 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
MIP lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301] Measured 10639.8 12117.3 1.13887
SEPT7 septin 7 (cdc10 protein homolog). [swissprot;acc:q16181] Rooted 113.374 123.463 1.08899
526 AQP2 aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181] Measured 10639.9 12117.4 1.13886
ETFB electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117] Squared 31189.6 37352.8 1.1976
RRP1 nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182] Ranked 250.538 234.401 1.06884
SEPT6 septin 6. [swissprot;acc:q14141] Rooted 113.169 123.23 1.0889
527 DDX31 dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779] Ranked 248.56 232.579 1.06871
DNASE2B deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233] Rooted 153.191 166.771 1.08865
LSM5 u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9] Squared 18011.9 21552.8 1.19659
PPM1B protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688] Measured 4775.11 5438.18 1.13886
528 AQP1 aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972] 10635.3 12111.4 1.13879
PPP2R1A serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153] Squared 10606 8868.81 1.19588
WIPF1 wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Rooted 66.941 72.7546 1.08685
YME1L1 yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263] Ranked 222.146 237.393 1.06864

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/