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 858 to 907 of 3206 in total
Rank
description
measured
expected
final
Hugo
858 SIGNAL TRANSDUCER AND ACTIVATOR OF TRANSCRIPTION 1-ALPHA/BETA (TRANSCRIPTION FACTOR ISGF-3 COMPONENTS P91/P84). [SWISSPROT;Acc:P42224] 0.331884 1.2742 0.260464605 STAT1
859 U4/U6 SMALL NUCLEAR RIBONUCLEOPROTEIN PRP4 (U4/U6 SNRNP 60 KDA PROTEIN) (WD SPLICING FACTOR PRP4) (HPRP4). [SWISSPROT;Acc:O43172] 0.0530266 0.203611 0.26043092 PRPF4
860 HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN K (HNRNP K) (DC-STRETCH BINDING PROTEIN) (CSBP) (TRANSFORMATION UPREGULATED NUCLEAR PROTEIN) (TUNP). [SWISSPROT;Acc:Q07244] 0.35663 1.36939 0.260429826 HNRPK
861 TWINKLE; LIKELY ORTHOLOG OF MOUSE T7 GP4-LIKE PROTEIN WITH INTRAMITOCHONDRIAL NUCLEOID LOCALIZATION. [RefSeq;Acc:NM_021830] 0.176631 0.678587 0.260292343 PEO1
862 0.0441578 0.169647 0.260292254 PYROXD1
863 "RABAPTIN, RAB GTPASE BINDING EFFECTOR PROTEIN 1; RABAPTIN-5; NEUROCRESCIN. [RefSeq;Acc:NM_004703]" RABEP1
864 40S RIBOSOMAL PROTEIN S30. [SWISSPROT;Acc:Q05472] 0.124733 0.479216 0.26028555 FAU
865 "PRESYNAPTIC PROTEIN SAP97 (SYNAPSE-ASSOCIATED PROTEIN 97) (DISCS, LARGE HOMOLOG 1) (HDLG). [SWISSPROT;Acc:Q12959]" 0.16564 0.636381 0.260284327 DLG1
866 "CHANNEL ASSOCIATED PROTEIN OF SYNAPSE-110 (CHAPSYN-110) (DISCS, LARGE HOMOLOG 2). [SWISSPROT;Acc:Q15700]" 0.141754 0.544635 0.260273394 DLG2
867 "PRESYNAPTIC PROTEIN SAP102 (SYNAPSE-ASSOCIATED PROTEIN 102) (NEUROENDOCRINE-DLG) (NE-DLG) (DISCS, LARGE HOMOLOG 3). [SWISSPROT;Acc:Q92796]" 0.138045 0.530387 0.260272216 DLG3
868 "PRESYNAPTIC DENSITY PROTEIN 95 (PSD-95) (DISCS, LARGE HOMOLOG 4) (POSTSYNAPTIC DENSITY-95). [SWISSPROT;Acc:P78352]" 0.138678 0.53282 0.260271762 DLG4
869 HOMEOBOX PROTEIN BARH-LIKE 1. [SWISSPROT;Acc:Q9HBU1] 0.139848 0.537326 0.260266579 BARX1
870 T-CELL LEUKEMIA HOMEOBOX PROTEIN 2 (HOMEOBOX PROTEIN HOX-11L1) (NEURAL CREST HOMEOBOX PROTEIN). [SWISSPROT;Acc:O43763] 0.0368198 0.14147 0.260265781 TLX2
871 T-CELL LEUKEMIA HOMEOBOX PROTEIN 3 (HOMEOBOX PROTEIN HOX-11L2). [SWISSPROT;Acc:O43711] 0.0457909 0.175939 0.260265774 TLX3
872 OPSIN 4 (MELANOPSIN). [SWISSPROT;Acc:Q9UHM6] 0.0585668 0.225027 0.260265657 OPN4
873 T-CELL LEUKEMIA HOMEOBOX PROTEIN 1 (HOMEOBOX PROTEIN HOX-11) (TCL-3 PROTO-ONCOGENE). [SWISSPROT;Acc:P31314] 0.0374306 0.143817 0.260265476 TLX1
874 HECT DOMAIN CONTAINING PROTEIN 1 (FRAGMENT). [SWISSPROT;Acc:Q9ULT8] 0.0211489 0.081259 0.260265324 HECTD1
875 HOMEOBOX PROTEIN BARH-LIKE 2. [SWISSPROT;Acc:Q9UMQ3] 0.109193 0.419545 0.260265287 BARX2
876 U6 SNRNA-ASSOCIATED SM-LIKE PROTEIN LSM5. [SWISSPROT;Acc:Q9Y4Y9] 0.196219 0.754024 0.260229117 LSM5
877 T54 PROTEIN. [SWISSPROT;Acc:Q92917] 0.314497 1.20911 0.260106194 GPKOW
878 PUTATIVE PRE-MRNA SPLICING FACTOR RNA HELICASE (ATP-DEPENDENT RNA HELICASE #3) (DEAH-BOX PROTEIN 16). [SWISSPROT;Acc:O60231] 0.039713 0.15268 0.260106104 no value
879 1.02292 3.93312 0.260078513 ARRDC2
880 DYNAMIN 1-LIKE PROTEIN ISOFORM 3; DYNAMIN-LIKE PROTEIN. [RefSeq;Acc:NM_005690] 0.121609 0.467587 0.260077804 DNM1L
881 "PHOSPHOINOSITIDE-3-KINASE, CLASS 2, ALPHA POLYPEPTIDE; C2-CONTAINING PHOSPHATIDYLINOSITOL KINASE. [RefSeq;Acc:NM_002645]" 0.0345092 0.132688 0.260077776 PIK3C2A
882 PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING GAMMA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-GAMMA) (PTDINS-3-KINASE C2 GAMMA) (PI3K-C2GAMMA). [SWISSPROT;Acc:O75747] 0.0242456 0.0932247 0.260076997 PIK3C2G
883 PHOSPHATIDYLINOSITOL-4-PHOSPHATE 3-KINASE C2 DOMAIN-CONTAINING BETA POLYPEPTIDE (EC 2.7.1.154) (PHOSPHOINOSITIDE 3-KINASE-C2-BETA) (PTDINS-3-KINASE C2 BETA) (PI3K-C2BETA) (C2-PI3K). [SWISSPROT;Acc:O00750] 0.0265832 0.102213 0.260076507 PIK3C2B
884 SCRIBBLE. [RefSeq;Acc:NM_015356] 0.163652 0.629348 0.260034194 SCRIB
885 LAP (LEUCINE-RICH REPEATS AND PDZ) AND NO PDZ PROTEIN. [RefSeq;Acc:NM_018214] 0.122677 0.471848 0.259992625 LRRC1
886 KINESIN HEAVY CHAIN ISOFORM 5C (KINESIN HEAVY CHAIN NEURON-SPECIFIC 2). [SWISSPROT;Acc:O60282] 0.152626 0.587298 0.25987829 KIF5C
887 KINESIN LIGHT CHAIN 2 (KLC 2). [SWISSPROT;Acc:Q9H0B6] 0.527178 2.02856 0.259877943 KLC2
888 EXOCYST COMPLEX COMPONENT SEC3 (BM-012). [SWISSPROT;Acc:Q9NV70] 0.0775579 0.29844 0.259877697 EXOC1
889 NEURONAL KINESIN HEAVY CHAIN (NKHC) (KINESIN HEAVY CHAIN ISOFORM 5A) (KINESIN HEAVY CHAIN NEURON-SPECIFIC 1). [SWISSPROT;Acc:Q12840] 0.131576 0.5063 0.259877543 KIF5A
890 TRANSCRIPTION FACTOR IIIA (FACTOR A) (TFIIIA). [SWISSPROT;Acc:Q92664] 0.0755679 0.290783 0.259877297 GTF3A
891 RHO-GTPASE-ACTIVATING PROTEIN 8. [SWISSPROT;Acc:Q9NSG0] 0.0962556 0.370389 0.259877048 PRR5
892 0.0770577 0.296516 0.259877039 TMEM53
893 RHO-GTPASE-ACTIVATING PROTEIN 1 (GTPASE-ACTIVATING PROTEIN RHOOGAP) (RHO-RELATED SMALL GTPASE PROTEIN ACTIVATOR) (CDC42 GTPASE-ACTIVATING PROTEIN) (P50-RHOGAP). [SWISSPROT;Acc:Q07960] 0.119625 0.460314 0.259876954 ARHGAP1
894 KINESIN HEAVY CHAIN (UBIQUITOUS KINESIN HEAVY CHAIN) (UKHC). [SWISSPROT;Acc:P33176] 0.131086 0.504416 0.259876768 KIF5B
895 KINESIN LIGHT CHAIN 1 (KLC 1). [SWISSPROT;Acc:Q07866] 0.684483 2.63388 0.259876304 KLC1
896 0.161768 0.623248 0.259556388 PRPF38B
897 VACUOLAR PROTEIN SORTING 18 (HVPS18). [SWISSPROT;Acc:Q9P253] 0.21331 0.821874 0.259541 VPS18
898 WILMS' TUMOR 1-ASSOCIATING PROTEIN (WT1-ASSOCIATED PROTEIN). [SWISSPROT;Acc:Q15007] 0.0746561 0.287738 0.259458605 WTAP
899 SIGNAL RECOGNITION PARTICLE 68 KDA PROTEIN (SRP68). [SWISSPROT;Acc:Q9UHB9] 0.193159 0.744637 0.259400218 SRP68
900 0.0403612 0.155595 0.259399081 TEX9
901 SPLICING FACTOR ARGININE/SERINE-RICH 11 (ARGININE-RICH 54 KDA NUCLEAR PROTEIN) (P54). [SWISSPROT;Acc:Q05519] 0.148259 0.571608 0.259371807 SFRS11
902 LIMBIC SYSTEM-ASSOCIATED MEMBRANE PROTEIN PRECURSOR (LSAMP). [SWISSPROT;Acc:Q13449] 0.128336 0.494891 0.25932175 LSAMP
903 OPIOID BINDING PROTEIN/CELL ADHESION MOLECULE PRECURSOR (OBCAM) (OPIOID-BINDING CELL ADHESION MOLECULE) (OPCML). [SWISSPROT;Acc:Q14982] 0.145116 0.560999 0.258674258 OPCML
904 PEPTIDYLPROLYL ISOMERASE-LIKE 4; CYCLOPHILIN-TYPE PEPTIDYL-PROLYL CIS-TRANS ISOMERASE; PPIASE; SEROLOGICALLY DEFINED BREAST CANCER ANTIGEN NY-BR-18. [RefSeq;Acc:NM_139126] 0.227308 0.879442 0.258468438 PPIL4
905 SIMILAR TO GLUCOSAMINE-PHOSPHATE N-ACETYLTRANSFERASE (HYPOTHETICAL PROTEIN FLJ33258). [SPTREMBL;Acc:Q96EK6] 0.29051 1.12415 0.258426367 GNPNAT1
906 DELTA-INTERACTING PROTEIN A (HEPATITIS DELTA ANTIGEN INTERACTING PROTEIN A). [SWISSPROT;Acc:Q15834] 0.24009 0.929064 0.258421379 CCDC85B
907 ORPHAN NUCLEAR RECEPTOR NR6A1 (GERM CELL NUCLEAR FACTOR) (GCNF) (RETINOID RECEPTOR-RELATED TESTIS SPECIFIC RECEPTOR) (RTR). [SWISSPROT;Acc:Q15406] 0.196675 0.76137 0.258317244 NR6A1

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/