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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measured Gene Rank expected description Hugo final
Results: HTML CSV LaTeX Showing element 1 to 50 of 3206 in total
measured
Rank
expected
description
Hugo
final
0.000173011 3206 0.7865 no value 0.000219976
0.000178236 3204 0.81025 ATLASTIN; GUANYLATE-BINDING PROTEIN 3. [RefSeq;Acc:NM_015915] 0.000219977
0.000571223 3205 2.59675 C1orf166 0.000219976
0.00386024 3199 0.104721 CHMP2B 0.036862138
0.0100954 3198 0.273869 PUTATIVE BREAST ADENOCARCINOMA MARKER (32KD). [RefSeq;Acc:NM_014453] CHMP2A 0.036862149
0.0131531 2631 0.0626341 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-6 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15825]" CHRNA6 0.209999026
0.0132921 2635 0.0632961 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-3 CHAIN PRECURSOR. [SWISSPROT;Acc:P32297]" CHRNA3 0.20999872
0.0139025 2163 0.0611788 PHOSPHOLIPID TRANSFER PROTEIN PRECURSOR (LIPID TRANSFER PROTEIN II). [SWISSPROT;Acc:P55058] PLTP 0.227243751
0.0139875 1813 0.059666 CARBOXYPEPTIDASE B PRECURSOR (EC 3.4.17.2) (PANCREAS-SPECIFIC PROTEIN) (PASP). [SWISSPROT;Acc:P15086] CPB1 0.234429994
0.0141571 2157 0.0622988 BPIL2 0.227245148
0.0142351 2630 0.0677865 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-2 CHAIN PRECURSOR. [SWISSPROT;Acc:Q15822]" CHRNA2 0.209999041
0.0142939 3192 0.387764 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM (AMSH) LIKE PROTEIN. [RefSeq;Acc:NM_020799] STAMBPL1 0.03686237
0.0145774 2932 0.0920202 REGULATOR OF G-PROTEIN SIGNALING 19 (RGS19) (G-ALPHA INTERACTING PROTEIN) (GAIP PROTEIN). [SWISSPROT;Acc:P49795] RGS19 0.158415218
0.0147736 2930 0.0932586 REGULATOR OF G-PROTEIN SIGNALING 17 (RGS17). [SWISSPROT;Acc:Q9UGC6] RGS17 0.158415417
0.0148857 2929 0.0939662 PUTATIVE RNA-BINDING PROTEIN 15 (RNA BINDING MOTIF PROTEIN 15) (ONE-TWENTY TWO PROTEIN). [SWISSPROT;Acc:Q96T37] RBM15 0.158415473
0.015194 2927 0.0959121 TRANSCRIPTION FACTOR LBX1. [SWISSPROT;Acc:P52954] LBX1 0.158415883
0.0153184 1619 0.063934 OLIGOPHRENIN 1. [SWISSPROT;Acc:O60890] OPHN1 0.239597084
0.0157159 2160 0.0691587 LIPOPOLYSACCHARIDE-BINDING PROTEIN PRECURSOR (LBP). [SWISSPROT;Acc:P18428] LBP 0.227244005
0.0163276 1623 0.0681463 ARHGAP10 0.23959628
0.0164226 1922 0.0707964 CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE B (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE B) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE B) (CT B) (CCT B) (CCT-BETA). [SWISSPROT;Acc:Q9Y5K3] PCYT1B 0.231969422
0.0166846 1733 0.0703876 "LIV-1 PROTEIN, ESTROGEN REGULATED. [RefSeq;Acc:NM_012319]" SLC39A6 0.23703891
0.0167203 2015 0.0725001 BRCA2 AND CDKN1A-INTERACTING PROTEIN ISOFORM BCCIPALPHA; BRCA2 AND CDKN1A-INTERACTING PROTEIN; CDK INHIBITOR P21 BINDING PROTEIN; BCCIPALPHA; BCCIPBETA; TOK-1ALPHA; TOK-1BETA. [RefSeq;Acc:NM_016567] BCCIP 0.230624509
0.016721 2067 0.0728736 RAS-RELATED PROTEIN RAB-26. [SWISSPROT;Acc:Q9ULW5] RAB26 0.229452092
0.0167711 1809 0.0715398 CARBOXYPEPTIDASE A5. [RefSeq;Acc:NM_080385] CPA5 0.234430345
0.0174686 3011 0.14338 LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR (LYMPHOCYTE IGE RECEPTOR) (FC-EPSILON-RII) (CD23) (BLAST-2) (IMMUNOGLOBULIN E-BINDING FACTOR). [SWISSPROT;Acc:P06734] FCER2 0.121834287
0.0174991 1916 0.0754368 BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 2 (PAPS SYNTHETHASE 2) (PAPSS 2) (SULFURYLASE KINASE 2) (SK2) (SK 2) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT no value 0.231970338
0.0175982 1727 0.0742417 "GLUTAMATE DECARBOXYLASE, 65 KDA ISOFORM (EC 4.1.1.15) (GAD-65) (65 KDA GLUTAMIC ACID DECARBOXYLASE). [SWISSPROT;Acc:Q05329]" GAD2 0.237039292
0.0179282 3195 0.486357 ASSOCIATED MOLECULE WITH THE SH3 DOMAIN OF STAM. [RefSeq;Acc:NM_006463] STAMBP 0.036862223
0.0184372 3175 0.333333 NIPA2 0.055311655
3176 C6orf130
3177 PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED; PUTATIVE GLIALBLASTOMA CELL DIFFERENTIATION-RELATED PROTEIN. [RefSeq;Acc:NM_016172] UBAC1
0.0186658 2632 0.0888852 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-4 CHAIN PRECURSOR. [SWISSPROT;Acc:P43681]" CHRNA4 0.209998965
0.018683 2933 0.117937 REGULATOR OF G-PROTEIN SIGNALING 20 (RGS20) (REGULATOR OF GZ- SELECTIVE PROTEIN SIGNALING 1) (GZ-SELECTIVE GTPASE-ACTIVATING PROTEIN) (G(Z)GAP). [SWISSPROT;Acc:O76081] RGS20 0.158415086
2934 RAP1 GTPASE-ACTIVATING PROTEIN 1 (RAP1GAP). [SWISSPROT;Acc:P47736] RAP1GAP
2935 CHROMOSOME 3P21.1 GENE SEQUENCE. [RefSeq;Acc:NM_013286] RBM15B
0.0187206 1917 0.0807026 NADPH-CYTOCHROME P450 REDUCTASE (EC 1.6.2.4) (CPR) (P450R). [SWISSPROT;Acc:P16435] POR 0.231970222
1918 BIFUNCTIONAL 3'-PHOSPHOADENOSINE 5'-PHOSPHOSULFATE SYNTHETHASE 1 (PAPS SYNTHETHASE 1) (PAPSS 1) (SULFURYLASE KINASE 1) (SK1) (SK 1) [INCLUDES: SULFATE ADENYLYLTRANSFERASE (EC 2.7.7.4) (SULFATE ADENYLATE TRANSFERASE) (SAT) (ATP-SULFURYLASE); ADENYLYLSULFAT PAPSS1
1919 CHOLINEPHOSPHATE CYTIDYLYLTRANSFERASE A (EC 2.7.7.15) (PHOSPHORYLCHOLINE TRANSFERASE A) (CTP:PHOSPHOCHOLINE CYTIDYLYLTRANSFERASE A) (CT A) (CCT A) (CCT-ALPHA). [SWISSPROT;Acc:P49585] PCYT1A
0.018755 2695 0.0901743 T-BOX TRANSCRIPTION FACTOR TBX6 (T-BOX PROTEIN 6). [SWISSPROT;Acc:O95947] TBX6 0.207986089
0.0189378 2633 0.0901805 STAR-RELATED LIPID TRANSFER PROTEIN 8 (STARD8) (START DOMAIN- CONTAINING PROTEIN 8). [SWISSPROT;Acc:Q92502] STARD8 0.209998836
0.0189917 1950 0.0821011 ESF1 0.231320896
0.0190828 1992 0.0826631 HYALURONAN SYNTHASE 1 (EC 2.4.1.212) (HYALURONATE SYNTHASE 1) (HYALURONIC ACID SYNTHASE 1) (HA SYNTHASE 1) (HUHAS1). [SWISSPROT;Acc:Q92839] HAS1 0.230850283
0.0191226 3040 0.174179 PANTOTHENATE KINASE 3 (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 3) (HPANK3). [SWISSPROT;Acc:Q9H999] PANK3 0.109787058
0.0193287 2320 0.0871461 MASPIN PRECURSOR (PROTEASE INHIBITOR 5). [SWISSPROT;Acc:P36952] no value 0.2217965
0.0193888 3037 0.176603 "PANTOTHENATE KINASE 2, MITOCHONDRIAL PRECURSOR (EC 2.7.1.33) (PANTOTHENIC ACID KINASE 2) (HPANK2). [SWISSPROT;Acc:Q9BZ23]" PANK2 0.109787489
0.0194204 2326 0.0875599 SERPIN B11. [SWISSPROT;Acc:Q96P15] no value 0.221795594
0.0194686 1961 0.0842001 ZINC FINGER PROTEIN 291. [SWISSPROT;Acc:Q9BY12] SCAPER 0.231218253
1963 0.0842002 MED11 0.231217978
1964 PEROXISOME BIOGENESIS FACTOR 1 (PEROXIN-1) (PEROXISOME BIOGENESIS DISORDER PROTEIN 1). [SWISSPROT;Acc:O43933] PEX1
0.0196287 2712 0.0946679 DELTA(14)-STEROL REDUCTASE (EC 1.3.1.70) (C-14 STEROL REDUCTASE) (STEROL C14-REDUCTASE) (DELTA14-SR) (TRANSMEMBRANE 7 SUPERFAMILY MEMBER 2) (ANOTHER NEW GENE 1) (PUTATIVE STEROL REDUCTASE SR-1). [SWISSPROT;Acc:O76062] TM7SF2 0.207342721

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/