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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Rank Gene description measured expected Hugo final
Results: HTML CSV LaTeX Showing element 802 to 851 of 3206 in total
Rank
description
measured
expected
Hugo
final
802 A KINDRED OF IGLON. [RefSeq;Acc:NM_173808] 0.099521 0.379834 NEGR1 0.262011826
803 TESTIS-SPECIFIC PROTEIN TEX28. [SWISSPROT;Acc:O15482] 0.0289523 0.1105 TEX28P2 0.262011765
804 ANKYRIN-REPEAT FAMILY A PROTEIN 2 (RFXANK-LIKE 2). [SWISSPROT;Acc:Q9H9E1] 0.15014 0.573028 ANKRA2 0.262011629
805 "ALPHA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-ALPHA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, ALPHA). [SWISSPROT;Acc:P54920]" 0.143723 0.548537 NAPA 0.262011496
806 27 KDA GOLGI SNARE PROTEIN (GOLGI SNAP RECEPTOR COMPLEX MEMBER 2) (MEMBRIN). [SWISSPROT;Acc:O14653] 0.1984 0.757219 GOSR2 0.262011386
807 MELANOMA ANTIGEN P15 (MELANOMA-ASSOCIATED ANTIGEN RECOGNIZED BY T LYMPHOCYTES). [SWISSPROT;Acc:Q13084] 0.0311416 0.118856 MRPL28 0.262011173
808 0.0305282 0.116515 TMCC1 0.2620109
809 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] 0.0371202 0.141681 ZMYND8 0.261998433
810 0.117829 0.450503 no value 0.261549868
811 BRAIN PROTEIN 16. [RefSeq;Acc:NM_016458] 0.0310375 0.118668 0.261549028
812 0.118571 0.453668 NKAP 0.261360731
813 DEAD-BOX PROTEIN ABSTRAKT HOMOLOG. [SWISSPROT;Acc:Q9UJV9] 0.0406169 0.155406 no value 0.261359922
814 0.0395402 0.151289 EXDL2 0.261355419
815 PEROXISOMAL MEMBRANE PROTEIN PEX14 (PEROXIN-14) (PEROXISOMAL MEMBRANE ANCHOR PROTEIN PEX14) (PTS1 RECEPTOR DOCKING PROTEIN). [SWISSPROT;Acc:O75381] 0.500223 1.91396 PEX14 0.261354992
816 ETHANOLAMINE-PHOSPHATE CYTIDYLYLTRANSFERASE (EC 2.7.7.14) (PHOSPHORYLETHANOLAMINE TRANSFERASE) (CTP:PHOSPHOETHANOLAMINE CYTIDYLYLTRANSFERASE). [SWISSPROT;Acc:Q99447] 0.278946 1.06742 PCYT2 0.261327313
817 "NADH-UBIQUINONE OXIDOREDUCTASE 13 KDA-A SUBUNIT, MITOCHONDRIAL PRECURSOR (EC 1.6.5.3) (EC 1.6.99.3) (COMPLEX I-13KD-A) (CI-13KD-A). [SWISSPROT;Acc:O75380]" 0.0296703 0.113537 NDUFS6 0.261327144
818 "MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE A ISOFORM (MLC1SA) (ALKALI). [SWISSPROT;Acc:P14649]" MYL6
819 "MYOSIN LIGHT CHAIN 1, SLOW-TWITCH MUSCLE B/VENTRICULAR ISOFORM (MLC1SB) (ALKALI). [SWISSPROT;Acc:P08590]" 0.025294 0.0967906 MYL3 0.26132703
820 "MYOSIN LIGHT CHAIN 1, EMBRYONIC MUSCLE/ATRIAL ISOFORM (PRO1957). [SWISSPROT;Acc:P12829]" 0.0259096 0.0991465 no value 0.261326421
821 "MYOSIN LIGHT CHAIN 1, SKELETAL MUSCLE ISOFORM (MLC1F) (A1 CATALYTIC) (ALKALI). [SWISSPROT;Acc:P05976]" 0.0255016 0.0975853 MYL1 0.261326245
822 PROTOCADHERIN FAT 2 PRECURSOR (HFAT2) (MULTIPLE EPIDERMAL GROWTH FACTOR-LIKE DOMAINS 1). [SWISSPROT;Acc:Q9NYQ8] 0.0300014 0.114826 FAT2 0.261277063
823 0.0385127 0.147402 TANC1 0.261276645
824 MLN 64 PROTEIN (STAR-RELATED LIPID TRANSFER PROTEIN 3) (STARD3) (START DOMAIN-CONTAINING PROTEIN 3) (CAB1 PROTEIN). [SWISSPROT;Acc:Q14849] STARD3
825 CADHERIN-RELATED TUMOR SUPPRESSOR HOMOLOG PRECURSOR (FAT PROTEIN HOMOLOG). [SWISSPROT;Acc:Q14517] FAT
826 MANNOSE-6-PHOSPHATE ISOMERASE (EC 5.3.1.8) (PHOSPHOMANNOSE ISOMERASE) (PMI) (PHOSPHOHEXOMUTASE). [SWISSPROT;Acc:P34949] 0.482651 1.84728 MPI 0.26127658
827 PUTATIVE ANKYRIN-REPEAT CONTAINING PROTEIN. [RefSeq;Acc:NM_025185] 0.0298281 0.114163 no value 0.261276421
828 MLN64 N-TERMINAL DOMAIN HOMOLOG (STARD3 N-TERMINAL LIKE PROTEIN). [SWISSPROT;Acc:O95772] 0.0299629 0.114679 STARD3NL 0.261276258
829 PURINE NUCLEOSIDE PHOSPHORYLASE (EC 2.4.2.1) (INOSINE PHOSPHORYLASE) (PNP). [SWISSPROT;Acc:P00491] 0.253043 0.969143 no value 0.261099755
830 KETOHEXOKINASE (EC 2.7.1.3) (HEPATIC FRUCTOKINASE). [SWISSPROT;Acc:P50053] 0.0303497 0.116238 KHK 0.26109964
831 "MALONYL-COA DECARBOXYLASE, MITOCHONDRIAL PRECURSOR (EC 4.1.1.9) (MCD). [SWISSPROT;Acc:O95822]" 0.0344093 0.131824 MLYCD 0.261024548
832 ITCHY HOMOLOG E3 UBIQUITIN PROTEIN LIGASE; ATROPHIN-1 INTERACTING PROTEIN 4; ITCHY (MOUSE HOMOLOG) E3 UBIQUITIN PROTEIN LIGASE; NFE2-ASSOCIATED POLYPEPTIDE 1; UBIQUITIN PROTEIN LIGASE ITCH. [RefSeq;Acc:NM_031483] 0.127743 0.489392 ITCH 0.261023883
833 KH-TYPE SPLICING REGULATORY PROTEIN (FUSE BINDING PROTEIN 2); KH-TYPE SPLICING REGULATORY PROTEIN (FUSE-BINDING PROTEIN 2). [RefSeq;Acc:NM_003685] 0.418445 1.60336 KHSRP 0.260980067
834 FAR UPSTREAM ELEMENT-BINDING PROTEIN; FAR UPSTREAM ELEMENT BINDING PROTEIN; FUSE-BINDING PROTEIN. [RefSeq;Acc:NM_003902] 0.353001 1.35261 FUBP1 0.260977665
835 FUSE BINDING PROTEIN 3 (FRAGMENT). [SPTREMBL;Acc:Q92946] 0.330618 1.26685 FUBP3 0.260976438
836 "PAIRED BOX PROTEIN PAX-6 (OCULORHOMBIN) (ANIRIDIA, TYPE II PROTEIN). [SWISSPROT;Acc:P26367]" 0.876793 3.36108 PAX6 0.260866448
837 0.152414 0.584621 SLC46A1 0.260705654
838 SLC46A3
839 LAMININ GAMMA-1 CHAIN PRECURSOR (LAMININ B2 CHAIN). [SWISSPROT;Acc:P11047] 0.386694 1.48326 LAMC1 0.260705473
840 FEM-1 HOMOLOG B; FEM-1-LIKE DEATH RECEPTOR BINDING PROTEIN; FEM-1 (C.ELEGANS) HOMOLOG B. [RefSeq;Acc:NM_015322] 0.845995 3.24503 FEM1B 0.260704832
841 LEUCINE-RICH REPEAT PROTEIN LRRC3 PRECURSOR. [SWISSPROT;Acc:Q9BY71] 0.0837034 0.321066 LRRC3 0.260704653
842 "NEURONAL ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA-7 CHAIN PRECURSOR. [SWISSPROT;Acc:P36544]" 0.077721 0.298119 CHRNA7 0.260704618
843 LEUCINE-RICH REPEAT-CONTAINING PROTEIN 15 PRECURSOR (HLIB). [SWISSPROT;Acc:Q8TF66] 0.0992922 0.380861 LRRC15 0.260704562
844 "ADENYLATE CYCLASE, TYPE V (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (ADENYLYL CYCLASE) (FRAGMENT). [SWISSPROT;Acc:O95622]" 0.162988 0.625183 ADCY5 0.260704466
845 "ADENYLATE CYCLASE, TYPE VI (EC 4.6.1.1) (ATP PYROPHOSPHATE-LYASE) (CA(2+)-INHIBITABLE ADENYLYL CYCLASE). [SWISSPROT;Acc:O43306]" 0.198584 0.761721 ADCY6 0.260704379
846 THYMIC STROMAL CO-TRANSPORTER. [RefSeq;Acc:NM_033051] 0.106987 0.410377 SLC46A2 0.260704182
847 0.0410035 0.157329 no value 0.260622644
848 SR RICH PROTEIN. [RefSeq;Acc:NM_032870] 0.479679 1.84052 SFRS18 0.260621455
849 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 5B. [SWISSPROT;Acc:P51692] 0.462971 1.77681 STAT5B 0.260563032
850 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 5A. [SWISSPROT;Acc:P42229] 0.449791 1.72628 STAT5A 0.260555066
851 CONSERVED OLIGOMERIC GOLGI COMPLEX COMPONENT 2 (LOW DENSITY LIPOPROTEIN RECEPTOR DEFECT C-COMPLEMENTING PROTEIN). [SWISSPROT;Acc:Q14746] 0.0723993 0.277887 COG2 0.260535038

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/