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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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expected Gene measured Rank Hugo description final
Results: HTML CSV LaTeX Showing element 352 to 401 of 3206 in total
expected
measured
Rank
Hugo
description
final
0.138898 0.0320499 2001 no value POLY (ADP-RIBOSE) GLYCOHYDROLASE. [RefSeq;Acc:NM_003631] 0.230744143
0.139062 0.0336999 1521 ASCC2 ASC-1 COMPLEX SUBUNIT P100. [RefSeq;Acc:NM_032204] 0.242337231
0.139064 0.0342893 1272 NKIRAS2 I-KAPPA-B-INTERACTING RAS-LIKE PROTEIN 2. [RefSeq;Acc:NM_017595] 0.246572082
0.139157 0.0337842 1494 ARFGEF1 BREFELDIN A-INHIBITED GUANINE NUCLEOTIDE-EXCHANGE PROTEIN 1 (BREFELDIN A-INHIBITED GEP 1) (P200 ARF-GEP1) (P200 ARF GUANINE NUCLEOTIDE EXCHANGE FACTOR). [SWISSPROT;Acc:Q9Y6D6] 0.242777582
0.139495 0.0379775 519 BCAS2 "BREAST CARCINOMA AMPLIFIED SEQUENCE 2; SPLICEOSOME ASSOCIATED PROTEIN, AMPLIFIED IN BREAST CANCER. [RefSeq;Acc:NM_005872]" 0.272249901
0.139564 0.024304 2905 PLEKHG2 0.174142329
0.139602 0.0367538 773 no value "SIRTUIN 7; SIR2-RELATED PROTEIN TYPE 7; SIRTUIN TYPE 7; SIRTUIN (SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG) 7; SILENT MATING TYPE INFORMATION REGULATION 2, S.CEREVISIAE, HOMOLOG 7; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION" 0.263275598
0.139616 0.0389719 377 CCDC12 0.279136345
0.13962 0.0338352 1518 SOCS1 SUPPRESSOR OF CYTOKINE SIGNALING 1 (SOCS-1) (JAK-BINDING PROTEIN) (JAB) (STAT INDUCED STAT INHIBITOR 1) (SSI-1) (TEC-INTERACTING PROTEIN 3) (TIP-3). [SWISSPROT;Acc:O15524] 0.242337774
1519 FKBP1A FK506-BINDING PROTEIN 1A (EC 5.2.1.8) (PEPTIDYL-PROLYL CIS-TRANS ISOMERASE) (PPIASE) (ROTAMASE) (12 KDA FKBP) (FKBP-12) (IMMUNOPHILIN FKBP12). [SWISSPROT;Acc:P20071]
0.139829 0.0396993 343 C16orf57 0.283913208
0.140116 0.034279 1378 GSK3B GLYCOGEN SYNTHASE KINASE-3 BETA (EC 2.7.1.37) (GSK-3 BETA). [SWISSPROT;Acc:P49841] 0.244647292
0.14013 0.0323264 2008 SUV39H2 "HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 2 (EC 2.1.1.43) (HISTONE H3-K9 METHYLTRANSFERASE 2) (H3-K9-HMTASE 2) (SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2) (SU(VAR)3-9 HOMOLOG 2). [SWISSPROT;Acc:Q9H5I1]" 0.230688646
0.140415 0.0316607 2204 NDST3 N-DEACETYLASE/N-SULFOTRANSFERASE (HEPARAN GLUCOSAMINYL) 3. [RefSeq;Acc:NM_004784] 0.225479472
0.140465 0.0337232 1599 IGBP1 IMMUNOGLOBULIN-BINDING PROTEIN 1 (CD79A-BINDING PROTEIN 1) (B CELL SIGNAL TRANSDUCTION MOLECULE ALPHA 4) (ALPHA 4 PROTEIN). [SWISSPROT;Acc:P78318] 0.240082583
0.140583 0.0380979 557 OXR1 OXIDATION RESISTANCE 1. [RefSeq;Acc:NM_181354] 0.270999338
0.140652 0.0335839 1671 MIER2 0.238773
0.140868 0.0308129 2407 ITM2B INTEGRAL MEMBRANE PROTEIN 2B (TRANSMEMBRANE PROTEIN BRI) [CONTAINS: ABRI/ADAN AMYLOID PEPTIDE]. [SWISSPROT;Acc:Q9Y287] 0.21873598
0.140933 0.0369504 788 GPATCH1 EVOLUTIONARILY CONSERVED G-PATCH DOMAIN CONTAINING. [RefSeq;Acc:NM_018025] 0.262184158
0.14106 0.0356563 1049 CLGN CALMEGIN PRECURSOR. [SWISSPROT;Acc:O14967] 0.252773997
0.14113 0.0336981 1670 MIER3 0.238773471
0.141189 0.030828500000000002 2413 no value 0.218349163
0.141385 0.0289586 2742 KIAA1012 TRS85 HOMOLOG. [SWISSPROT;Acc:Q9Y2L5] 0.204820879
0.14147 0.0368198 870 TLX2 T-CELL LEUKEMIA HOMEOBOX PROTEIN 2 (HOMEOBOX PROTEIN HOX-11L1) (NEURAL CREST HOMEOBOX PROTEIN). [SWISSPROT;Acc:O43763] 0.260265781
0.141529 0.0319117 2205 NDST4 N-DEACETYLASE/N-SULFOTRANSFERASE 4. [RefSeq;Acc:NM_022569] 0.225478171
0.141553 0.0427222 281 RPE65 RETINAL PIGMENT EPITHELIUM-SPECIFIC PROTEIN 65KDA; RETINAL PIGMENT EPITHELIUM-SPECIFIC PROTEIN (65KD); RETINITIS PIGMENTOSA 20 (AUTOSOMAL RECESSIVE). [RefSeq;Acc:NM_000329] 0.301810629
0.141665 0.036112 999 B3GNT1 "N-ACETYLLACTOSAMINIDE BETA-1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE (EC 2.4.1.149) (POLY-N-ACETYLLACTOSAMINE EXTENSION ENZYME) (I-BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE) (IGNT) (UDP-GLCNAC:BETAGAL BETA- 1,3-N-ACETYLGLUCOSAMINYLTRANSFERASE 6). [SWISSP" 0.254911234
0.141681 0.0371202 809 ZMYND8 PROTEIN KINASE C BINDING PROTEIN 1 (RACK7) (CUTANEOUS T-CELL LYMPHOMA ASSOCIATED ANTIGEN SE14-3) (CTCL TUMOR ANTIGEN SE14-3) (ZINC FINGER MYND DOMAIN CONTAINING PROTEIN 8). [SWISSPROT;Acc:Q9ULU4] 0.261998433
0.142004 0.0327033 2026 C3orf23 0.230298442
0.142049 0.0331615 1852 no value PRESENILIN-LIKE PROTEIN 1 (EC 3.4.99.-) (SPPL2B PROTEIN). [SWISSPROT;Acc:Q8TCT7] 0.233451133
1853
0.142223 0.0385424 553 LATS2 "LATS, LARGE TUMOR SUPPRESSOR, HOMOLOG 2; LATS (LARGE TUMOR SUPPRESSOR, DROSOPHILA) HOMOLOG 2. [RefSeq;Acc:NM_014572]" 0.270999768
0.142328 0.0429558 294 no value "BETA-CAROTENE DIOXYGENASE 2; PUTATIVE B,B-CAROTENE-9',10'-DIOXYGENASE. [RefSeq;Acc:NM_031938]" 0.301808499
0.142333 0.0340138 1650 CABC1 "CHAPERONE-ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL PRECURSOR (CHAPERONE-ABC1-LIKE). [SWISSPROT;Acc:Q8NI60]" 0.238973393
1651 ADCK1 AARF DOMAIN CONTAINING KINASE 1. [RefSeq;Acc:NM_020421]
1652 ADCK2 AARF DOMAIN CONTAINING KINASE 2; PUTATIVE UBIQUINONE BIOSYNTHESIS PROTEIN AARF. [RefSeq;Acc:NM_052853]
0.142498 0.0338955 1699 ASNSD1 HCV NS3-TRANSACTIVATED PROTEIN 1. [RefSeq;Acc:NM_019048] 0.237866496
0.142608 0.0325606 2107 FBXO42 0.228322394
0.142675 0.0349958 1338 SRPK2 SFRS PROTEIN KINASE 2 ISOFORM B. [RefSeq;Acc:NM_182691] 0.245283336
0.143236 0.0366052 970 PERLD1 CAB2. [RefSeq;Acc:NM_033419] 0.255558658
0.143261 0.0394844 456 ZMAT2 0.275611646
0.14338 0.0174686 3011 FCER2 LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR (LYMPHOCYTE IGE RECEPTOR) (FC-EPSILON-RII) (CD23) (BLAST-2) (IMMUNOGLOBULIN E-BINDING FACTOR). [SWISSPROT;Acc:P06734] 0.121834287
0.143472 0.0397949 424 ARHGAP23 0.277370497
0.143817 0.0374306 873 TLX1 T-CELL LEUKEMIA HOMEOBOX PROTEIN 1 (HOMEOBOX PROTEIN HOX-11) (TCL-3 PROTO-ONCOGENE). [SWISSPROT;Acc:P31314] 0.260265476
0.144067 0.0377474 792 TMCC2 0.262012813
0.144194 0.0378601 784 no value 0.26256363
0.144696 0.0436706 290 NXNL1 0.301809311
0.14474 0.0326359 2203 NDST1 HEPARAN SULFATE N-DEACETYLASE/N-SULFOTRANSFERASE (EC 2.8.2.8) (N-HSST) (HSNST) ([HEPARAN SULFATE]-GLUCOSAMINE N-SULFOTRANSFERASE) (N-HEPARAN SULFATE SULFOTRANSFERASE) (GLUCOSAMINYL N-DEACETYLASE/N- SULFOTRANSFERASE). [SWISSPROT;Acc:P52848] 0.22547948
0.144924 0.0437393 293 PNMT PHENYLETHANOLAMINE N-METHYLTRANSFERASE (EC 2.1.1.28) (PNMTASE) (NORADRENALINE N-METHYLTRANSFERASE). [SWISSPROT;Acc:P11086] 0.301808534
0.14496 0.0314703 2445 UBL4B 0.21709644

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/