Decoding ENCODE. Jim Kent University of California Santa Cruz. ENCODE Timeline. ENCyclopedia of Dna Elements. Attempt to catalog as many functional elements in human genome as possible using current technologies. Pilot project - finished 2007, covered 1% of genome.
University of California Santa Cruz
List of mouse chromatin subtracks….
Signal densities of entire mouse chromatin data set.
Selected fields from related tables results: Ensemble Gene (ensGene) and Superfamily Description (sfDescription).
681/3329 (20%) of Ensemble not known also not conserved
1728/33,666 (5%) of Ensembl in general not conserved
Cytochrome P450 - a gene family important in drug metabolism.
The family is related in many ways. Sorted by protein homology
Various sorting methods let you focus on different types
of relationships between genes.
Sorting by gene distance is a quick way to browse candidate
genes in a region.
Clicking on row # or gene name selects that gene.
Configuration page controls column order and display options.
Also you can upload your own columns here.
Controlling expression display
GNF Atlas 2 column in ‘median of replicates’ mode. Actual
Column includes 79 tissues, slide only fits first half.
Sorting based on expression similarity to selected gene.
The filters page turns the Family Browser into a powerful
data mining tool.
Candidate Pancreatic Islet Membrane Genes
GO-annotated membrane proteins that are expressed at least 8X in pancreatic islets cells and no more than 4X elsewhere outside of pancreas and central nervous system. These might be good candidates for targets of the autoimmune response that can cause Type I diabetes.
The Sordid Details of the UCSC Genome Informatics Code Base
Download via http://genome.ucsc.edu/admin/cvs.html
Many modules require MySQL to be installed.
/* A dna sequence in one-letter-per-base format. */
struct dnaSeq *next; /* Next in list. */
char *name; /* Sequence name. */
char *dna; /* a’s c’s g’s and t’s. Null terminated */
int size; /* Number of bases. */
struct dnaSeq *dnaSeqFromString(char *string);
/* Convert string containing sequence and possibly
* white space and numbers to a dnaSeq. */
void dnaSeqFree(struct dnaSeq **pSeq);
/* Free dnaSeq and set pointer to NULL. */
void dnaSeqFreeList(struct dnaSeq **pList);
/* Free list of dnaSeq’s. */
/* A two dimensional object in a sleazy video game. */
struct screenObj *next; /* Next in list. */
char *name; /* Object name. */
int x,y,width,height; /* Bounds of object. */
void (*draw)(struct screenObj *obj); /* Draw object */
boolean (*in)(struct screenObj *obj, int x, int y);
/* Return true if x,y is in object */
void *custom; /* Custom data for a particular type */
void (*freeCustom)(struct screenObj *obj);
/* Free custom data. */
#define screenObjDraw(obj) (obj->draw(obj))
/* Draw object. */
void screenObjFree(struct screenObj **pObj);
/* Free up screen object including custom part. */
struct exoFish *exoFishLoad(char **row)
/* Load a exoFish from row fetched with select * from exoFish
* from database. Dispose of this with exoFishFree(). */
struct exoFish *ret;
ret->chrom = cloneString(row);
ret->chromStart = sqlUnsigned(row);
ret->chromEnd = sqlUnsigned(row);
ret->name = cloneString(row);
ret->score = sqlUnsigned(row);
"An evolutionarily conserved region (ecore) with Tetroadon"
string chrom; "Human chromosome or FPC contig"
uint chromStart; "Start position in chromosome"
uint chromEnd; "End position in chromosome"
string name; "Ecore name in Genoscope database"
uint score; "Score from 0 to 1000"
See autoSql.doc for more details.