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

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/