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 final Hugo
Results: HTML CSV LaTeX Showing element 758 to 807 of 3206 in total
Rank
description
measured
expected
final
Hugo
758 43 KDA RECEPTOR-ASSOCIATED PROTEIN OF THE SYNAPSE (RAPSYN) (ACETYLCHOLINE RECEPTOR-ASSOCIATED 43 KDA PROTEIN) (43 KDA POSTSYNAPTIC PROTEIN). [SWISSPROT;Acc:Q13702] 0.552551 2.09375 0.263904955 RAPSN
759 C1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN-LIKE PROTEIN ISOFORM 2; PUTATIVE PROTEIN TYROSINE PHOSPHATASE; C1 DOMAIN-CONTAINING PHOSPHATASE AND TENSIN-LIKE PROTEIN; TENSIN 2. [RefSeq;Acc:NM_015319] 0.260485 0.987283 0.263840257 TENC1
760 TUMOR ENDOTHELIAL MARKER 6; THYROID SPECIFIC PTB DOMAIN PROTEIN; TENSIN 3. [RefSeq;Acc:NM_022748] 0.283226 1.0738 0.263760477 TNS3
761 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-1 (DISHEVELLED-1) (DSH HOMOLOG 1). [SWISSPROT;Acc:O14640] 0.217793 0.825859 0.26371693 DVL1
762 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-2 (DISHEVELLED-2) (DSH HOMOLOG 2). [SWISSPROT;Acc:O14641] 0.223153 0.846393 0.263651755 DVL2
763 RAB COUPLING PROTEIN; RAB-INTERACTING RECYCLING PROTEIN; RAB EFFECTOR PROTEIN; RAB11-FAMILY INTERACTING PROTEIN 1. [RefSeq;Acc:NM_025151] 0.0360283 0.136657 0.263640355 RAB11FIP1
764 POTENTIAL PHOSPHOLIPID-TRANSPORTING ATPASE IIA (EC 3.6.1.-). [SWISSPROT;Acc:O75110] 0.0460867 0.174809 0.263640316 ATP9A
765 GAMMA-SNAP-ASSOCIATED FACTOR 1; RAB11-INTERACTING PROTEIN. [RefSeq;Acc:NM_015470] RAB11FIP5
766 PROTEIN C14ORF122 (CGI-112). [SWISSPROT;Acc:Q9Y3B6] 0.0365698 0.138711 0.26364023 C14orf122
767 0.0355674 0.134909 0.263639935 RAB11FIP2
768 DPY-30-LIKE PROTEIN. [SWISSPROT;Acc:Q9C005] 0.3486 1.32226 0.263639526 no value
769 NEIGHBOR OF COX4. [SWISSPROT;Acc:O43402] 0.0269837 0.102351 0.263638851 COX4NB
770 HSP90 CO-CHAPERONE CDC37 (HSP90 CHAPERONE PROTEIN KINASE-TARGETING SUBUNIT) (P50CDC37). [SWISSPROT;Acc:Q16543] 0.188365 0.715239 0.26335952 CDC37
771 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-3 (DISHEVELLED-3) (DSH HOMOLOG 3). [SWISSPROT;Acc:Q92997] 0.256243 0.973151 0.263312682 DVL3
772 CASEIN KINASE II BETA CHAIN (CK II) (PHOSVITIN) (G5A). [SWISSPROT;Acc:P13862] 0.492676 1.87133 0.263275852 no value
773 "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" 0.0367538 0.139602 0.263275598
774 TARGET OF MYB1-LIKE 2; TARGET OF MYB1 (CHICKEN) HOMOLOG-LIKE 2. [RefSeq;Acc:NM_144678] 0.179057 0.680239 0.263226601 TOM1L2
775 TRIPLE FUNCTIONAL DOMAIN PROTEIN (PTPRF INTERACTING PROTEIN). [SWISSPROT;Acc:O75962] 0.0734189 0.278919 0.2632266 TRIO
776 TARGET OF MYB PROTEIN 1. [SWISSPROT;Acc:O60784] 0.230424 0.875383 0.263226496 TOM1
777 HUNTINGTIN-ASSOCIATED PROTEIN-INTERACTING PROTEIN (DUO PROTEIN). [SWISSPROT;Acc:O60229] 0.0568574 0.216002 0.263226266 no value
778 ARP2/3 COMPLEX 34 KDA SUBUNIT (P34-ARC) (ACTIN-RELATED PROTEIN 2/3 COMPLEX SUBUNIT 2). [SWISSPROT;Acc:O15144] 0.427564 1.62441 0.263211874 ARPC2
779 TENSIN. [RefSeq;Acc:NM_022648] 0.320357 1.21727 0.263176617 TNS1
780 RNA-BINDING REGION CONTAINING PROTEIN 2 (HEPATOCELLULAR CARCINOMA PROTEIN 1) (SPLICING FACTOR HCC1). [SWISSPROT;Acc:Q14498] 0.349158 1.32674 0.263169875 RBM39
781 "NUCLEAR FACTOR, INTERLEUKIN 3 REGULATED. [RefSeq;Acc:NM_005384]" 0.150787 0.573002 0.263152659 NFIL3
782 SYNTAXIN 12. [RefSeq;Acc:NM_177424] 0.206261 0.78389 0.263124928 STX12
783 WW DOMAIN BINDING PROTEIN 2 (WBP-2). [SWISSPROT;Acc:Q969T9] 0.0979343 0.372839 0.262671823 WBP2
784 0.0378601 0.144194 0.26256363 no value
785 BREAST CANCER TYPE 1 SUSCEPTIBILITY PROTEIN. [SWISSPROT;Acc:P38398] 0.11358 0.432583 0.262562329 BRCA1
786 SYNTAXIN 7. [SWISSPROT;Acc:O15400] 0.209282 0.797115 0.262549318 STX7
787 CBF1 INTERACTING COREPRESSOR. [RefSeq;Acc:NM_004882] 0.363013 1.38457 0.262184649 no value
788 EVOLUTIONARILY CONSERVED G-PATCH DOMAIN CONTAINING. [RefSeq;Acc:NM_018025] 0.0369504 0.140933 0.262184158 GPATCH1
789 ADENOVIRUS 5 E1A-BINDING PROTEIN (BS69 PROTEIN). [SWISSPROT;Acc:Q15326] 0.0552487 0.210853 0.262024728 ZMYND11
790 SYNTAXIN 16 (SYN16). [SWISSPROT;Acc:O14662] 0.279039 1.06498 0.262013371 STX16
791 SYNTAXIN 1A (NEURON-SPECIFIC ANTIGEN HPC-1). [SWISSPROT;Acc:Q16623] 0.147338 0.562331 0.262012943 STX1A
792 0.0377474 0.144067 0.262012813 TMCC2
793 "BETA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-BETA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, BETA). [SWISSPROT;Acc:Q9H115]" 0.129493 0.494224 0.262012772 NAPB
794 INFLAMMATION-RELATED G PROTEIN-COUPLED RECEPTOR EX33. [RefSeq;Acc:NM_020370] 0.0690966 0.263715 0.2620124 GPR84
795 PALMITOYL-PROTEIN THIOESTERASE 1 PRECURSOR (EC 3.1.2.22) (PALMITOYL- PROTEIN HYDROLASE 1). [SWISSPROT;Acc:P50897] PPT1
796 SIMILAR TO NUCLEAR PROTEIN E3-3 ORF1. [SPTREMBL;Acc:Q9BU61] C3orf60
797 ADIPOCYTE PLASMA MEMBRANE-ASSOCIATED PROTEIN (BSCV PROTEIN). [SWISSPROT;Acc:Q9HDC9] 0.0870266 0.332147 0.262012302 C20orf3
798 0.0312832 0.119396 0.262012128 TMCC3
799 SYNAPTOSOMAL-ASSOCIATED PROTEIN 29 (SNAP-29) (VESICLE-MEMBRANE FUSION PROTEIN SNAP-29) (SOLUBLE 29 KDA NSF ATTACHMENT PROTEIN). [SWISSPROT;Acc:O95721] 0.14026 0.535319 0.262011997 SNAP29
800 SYNTAXIN 1B. [SWISSPROT;Acc:Q15531] 0.120499 0.459899 0.262011877 STX1B
801 DNA-BINDING PROTEIN RFXANK (REGULATORY FACTOR X SUBUNIT B) (RFX-B) (ANKYRIN REPEAT FAMILY A PROTEIN 1). [SWISSPROT;Acc:O14593] 0.182131 0.695125 0.262011868 RFXANK
802 A KINDRED OF IGLON. [RefSeq;Acc:NM_173808] 0.099521 0.379834 0.262011826 NEGR1
803 TESTIS-SPECIFIC PROTEIN TEX28. [SWISSPROT;Acc:O15482] 0.0289523 0.1105 0.262011765 TEX28P2
804 ANKYRIN-REPEAT FAMILY A PROTEIN 2 (RFXANK-LIKE 2). [SWISSPROT;Acc:Q9H9E1] 0.15014 0.573028 0.262011629 ANKRA2
805 "ALPHA-SOLUBLE NSF ATTACHMENT PROTEIN (SNAP-ALPHA) (N-ETHYLMALEIMIDE- SENSITIVE FACTOR ATTACHMENT PROTEIN, ALPHA). [SWISSPROT;Acc:P54920]" 0.143723 0.548537 0.262011496 NAPA
806 27 KDA GOLGI SNARE PROTEIN (GOLGI SNAP RECEPTOR COMPLEX MEMBER 2) (MEMBRIN). [SWISSPROT;Acc:O14653] 0.1984 0.757219 0.262011386 GOSR2
807 MELANOMA ANTIGEN P15 (MELANOMA-ASSOCIATED ANTIGEN RECOGNIZED BY T LYMPHOCYTES). [SWISSPROT;Acc:Q13084] 0.0311416 0.118856 0.262011173 MRPL28

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/